Update README

.github/dependabot.yml

@@ -1,12 +0,0 @@
-# To get started with Dependabot version updates, you'll need to specify which
-# package ecosystems to update and where the package manifests are located.
-# Please see the documentation for all configuration options:
-# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
-
-version: 2
-updates:
-  - package-ecosystem: "" # See documentation for possible values
-    directory: "/" # Location of package manifests
-    schedule:
-      interval: "weekly"
-      

.github/workflows/claude-code-actions.yml

@@ -1,16 +0,0 @@
-name: Claude Code Integration
-
-on:
-  issue_comment:
-    types: [ created ]
-  pull_request_review_comment:
-    types: [ created ]
-
-jobs:
-  claude-integration:
-    uses: basicmachines-co/claude-code-github-action/.github/workflows/claude-full.yml@v0.11.0
-    with:
-      issue-label: 'claude-fix'  # Optional: customize the trigger label
-    secrets:
-      ANTHROPIC_API_KEY: ${{ secrets.ANTHROPIC_API_KEY }}
-      PERSONAL_ACCESS_TOKEN: ${{ secrets.CLAUDE_TOKEN }}

.github/workflows/test.yml

@@ -5,12 +5,6 @@ on:
     branches: [ "main" ]
   pull_request:
     branches: [ "main" ]
-  # pull_request_target runs on the BASE of the PR, not the merge result.
-  # It has write permissions and access to secrets.
-  # It's useful for PRs from forks or automated PRs but requires careful use for security reasons.
-  # See: https://docs.github.com/en/actions/using-workflows/events-that-trigger-workflows#pull_request_target
-  pull_request_target:
-    branches: [ "main" ]
 
 jobs:
   test:

.gitignore

@@ -46,9 +46,4 @@ ENV/
 
 # obsidian docs:
 /docs/.obsidian/
-/examples/.obsidian/
-/examples/.basic-memory/
-
-
-# claude action
-claude-output
+/examples/.obsidian/

CHANGELOG.md

@@ -1,319 +1,6 @@
 # CHANGELOG
 
 
-## v0.12.3 (2025-04-17)
-
-### Bug Fixes
-
-- Add extra logic for permalink generation with mixed Latin unicode and Chinese characters
-  ([`73ea91f`](https://github.com/basicmachines-co/basic-memory/commit/73ea91fe0d1f7ab89b99a1b691d59fe608b7fcbb))
-
-Signed-off-by: phernandez <paul@basicmachines.co>
-
-- Modify recent_activity args to be strings instead of enums
-  ([`3c1cc34`](https://github.com/basicmachines-co/basic-memory/commit/3c1cc346df519e703fae6412d43a92c7232c6226))
-
-Signed-off-by: phernandez <paul@basicmachines.co>
-
-
-## v0.12.2 (2025-04-08)
-
-### Bug Fixes
-
-- Utf8 for all file reads/write/open instead of default platform encoding
-  ([#91](https://github.com/basicmachines-co/basic-memory/pull/91),
-  [`2934176`](https://github.com/basicmachines-co/basic-memory/commit/29341763318408ea8f1e954a41046c4185f836c6))
-
-Signed-off-by: phernandez <paul@basicmachines.co>
-
-
-## v0.12.1 (2025-04-07)
-
-### Bug Fixes
-
-- Run migrations and sync when starting mcp
-  ([#88](https://github.com/basicmachines-co/basic-memory/pull/88),
-  [`78a3412`](https://github.com/basicmachines-co/basic-memory/commit/78a3412bcff83b46e78e26f8b9fce42ed9e05991))
-
-
-## v0.12.0 (2025-04-06)
-
-### Bug Fixes
-
-- [bug] `#` character accumulation in markdown frontmatter tags prop
-  ([#79](https://github.com/basicmachines-co/basic-memory/pull/79),
-  [`6c19c9e`](https://github.com/basicmachines-co/basic-memory/commit/6c19c9edf5131054ba201a109b37f15c83ef150c))
-
-- [bug] Cursor has errors calling search tool
-  ([#78](https://github.com/basicmachines-co/basic-memory/pull/78),
-  [`9d581ce`](https://github.com/basicmachines-co/basic-memory/commit/9d581cee133f9dde4a0a85118868227390c84161))
-
-- [bug] Some notes never exit "modified" status
-  ([#77](https://github.com/basicmachines-co/basic-memory/pull/77),
-  [`7930ddb`](https://github.com/basicmachines-co/basic-memory/commit/7930ddb2919057be30ceac8c4c19da6aaa1d3e92))
-
-- [bug] write_note Tool Fails to Update Existing Files in Some Situations.
-  ([#80](https://github.com/basicmachines-co/basic-memory/pull/80),
-  [`9bff1f7`](https://github.com/basicmachines-co/basic-memory/commit/9bff1f732e71bc60f88b5c2ce3db5a2aa60b8e28))
-
-- Set default mcp log level to ERROR
-  ([#81](https://github.com/basicmachines-co/basic-memory/pull/81),
-  [`248214c`](https://github.com/basicmachines-co/basic-memory/commit/248214cb114a269ca60ff6398e382f9e2495ad8e))
-
-- Write_note preserves frontmatter fields in content
-  ([#84](https://github.com/basicmachines-co/basic-memory/pull/84),
-  [`3f4d9e4`](https://github.com/basicmachines-co/basic-memory/commit/3f4d9e4d872ebc0ed719c61b24d803c14a9db5e6))
-
-### Documentation
-
-- Add VS Code instructions to README
-  ([#76](https://github.com/basicmachines-co/basic-memory/pull/76),
-  [`43cbb7b`](https://github.com/basicmachines-co/basic-memory/commit/43cbb7b38cc0482ac0a41b6759320e3588186e43))
-
-- Updated basicmachines.co links to be https
-  ([#69](https://github.com/basicmachines-co/basic-memory/pull/69),
-  [`40ea28b`](https://github.com/basicmachines-co/basic-memory/commit/40ea28b0bfc60012924a69ecb76511daa4c7d133))
-
-### Features
-
-- Add watch to mcp process ([#83](https://github.com/basicmachines-co/basic-memory/pull/83),
-  [`00c8633`](https://github.com/basicmachines-co/basic-memory/commit/00c8633cfcee75ff640ff8fe81dafeb956281a94))
-
-- Permalink enhancements ([#82](https://github.com/basicmachines-co/basic-memory/pull/82),
-  [`617e60b`](https://github.com/basicmachines-co/basic-memory/commit/617e60bda4a590678a5f551f10a73e7b47e3b13e))
-
-- Avoiding "useless permalink values" for files without metadata - Enable permalinks to be updated
-  on move via config setting
-
-
-## v0.11.0 (2025-03-29)
-
-### Bug Fixes
-
-- Just delete db for reset db instead of using migrations.
-  ([#65](https://github.com/basicmachines-co/basic-memory/pull/65),
-  [`0743ade`](https://github.com/basicmachines-co/basic-memory/commit/0743ade5fc07440f95ecfd816ba7e4cfd74bca12))
-
-Signed-off-by: phernandez <paul@basicmachines.co>
-
-- Make logs for each process - mcp, sync, cli
-  ([#64](https://github.com/basicmachines-co/basic-memory/pull/64),
-  [`f1c9570`](https://github.com/basicmachines-co/basic-memory/commit/f1c95709cbffb1b88292547b0b8f29fcca22d186))
-
-Signed-off-by: phernandez <paul@basicmachines.co>
-
-### Documentation
-
-- Update broken "Multiple Projects" link in README.md
-  ([#55](https://github.com/basicmachines-co/basic-memory/pull/55),
-  [`3c68b7d`](https://github.com/basicmachines-co/basic-memory/commit/3c68b7d5dd689322205c67637dca7d188111ee6b))
-
-### Features
-
-- Add bm command alias for basic-memory
-  ([#67](https://github.com/basicmachines-co/basic-memory/pull/67),
-  [`069c0a2`](https://github.com/basicmachines-co/basic-memory/commit/069c0a21c630784e1bf47d2b7de5d6d1f6fadd7a))
-
-Signed-off-by: phernandez <paul@basicmachines.co>
-
-- Rename search tool to search_notes
-  ([#66](https://github.com/basicmachines-co/basic-memory/pull/66),
-  [`b278276`](https://github.com/basicmachines-co/basic-memory/commit/b27827671dc010be3e261b8b221aca6b7f836661))
-
-Signed-off-by: phernandez <paul@basicmachines.co>
-
-
-## v0.10.1 (2025-03-25)
-
-### Bug Fixes
-
-- Make set_default_project also activate project for current session to fix #37
-  ([`cbe72be`](https://github.com/basicmachines-co/basic-memory/commit/cbe72be10a646c0b03931bb39aff9285feae47f9))
-
-This change makes the 'basic-memory project default <name>' command both: 1. Set the default project
-  for future invocations (persistent change) 2. Activate the project for the current session
-  (immediate change)
-
-Added tests to verify this behavior, which resolves issue #37 where the project name and path
-  weren't changing properly when the default project was changed.
-
-🤖 Generated with [Claude Code](https://claude.ai/code)
-
-Co-Authored-By: Claude <noreply@anthropic.com>
-
-- Make set_default_project also activate project for current session to fix #37
-  ([`46c4fd2`](https://github.com/basicmachines-co/basic-memory/commit/46c4fd21645b109af59eb2a0201c7bd849b34a49))
-
-This change makes the 'basic-memory project default <name>' command both: 1. Set the default project
-  for future invocations (persistent change) 2. Activate the project for the current session
-  (immediate change)
-
-Added tests to verify this behavior, which resolves issue #37 where the project name and path
-  weren't changing properly when the default project was changed.
-
-🤖 Generated with [Claude Code](https://claude.ai/code)
-
-Co-Authored-By: Claude <noreply@anthropic.com>
-
-Signed-off-by: phernandez <paul@basicmachines.co>
-
-- Move ai_assistant_guide.md into package resources to fix #39
-  ([`390ff9d`](https://github.com/basicmachines-co/basic-memory/commit/390ff9d31ccee85bef732e8140b5eeecd7ee176f))
-
-This change relocates the AI assistant guide from the static directory into the package resources
-  directory, ensuring it gets properly included in the distribution package and is accessible when
-  installed via pip/uv.
-
-🤖 Generated with [Claude Code](https://claude.ai/code)
-
-Co-Authored-By: Claude <noreply@anthropic.com>
-
-- Move ai_assistant_guide.md into package resources to fix #39
-  ([`cc2cae7`](https://github.com/basicmachines-co/basic-memory/commit/cc2cae72c14b380f78ffeb67c2261e4dbee45faf))
-
-This change relocates the AI assistant guide from the static directory into the package resources
-  directory, ensuring it gets properly included in the distribution package and is accessible when
-  installed via pip/uv.
-
-🤖 Generated with [Claude Code](https://claude.ai/code)
-
-Co-Authored-By: Claude <noreply@anthropic.com>
-
-Signed-off-by: phernandez <paul@basicmachines.co>
-
-- Preserve custom frontmatter fields when updating notes
-  ([`78f234b`](https://github.com/basicmachines-co/basic-memory/commit/78f234b1806b578a0a833e8ee4184015b7369a97))
-
-Fixes #36 by modifying entity_service.update_entity() to read existing frontmatter from files before
-  updating them. Custom metadata fields such as Status, Priority, and Version are now preserved when
-  notes are updated through the write_note MCP tool.
-
-Added test case that verifies this behavior by creating a note with custom frontmatter and then
-  updating it.
-
-🤖 Generated with [Claude Code](https://claude.ai/code)
-
-Co-Authored-By: Claude <noreply@anthropic.com>
-
-- Preserve custom frontmatter fields when updating notes
-  ([`e716946`](https://github.com/basicmachines-co/basic-memory/commit/e716946b4408d017eca4be720956d5a210b4e6b1))
-
-Fixes #36 by modifying entity_service.update_entity() to read existing frontmatter from files before
-  updating them. Custom metadata fields such as Status, Priority, and Version are now preserved when
-  notes are updated through the write_note MCP tool.
-
-Added test case that verifies this behavior by creating a note with custom frontmatter and then
-  updating it.
-
-🤖 Generated with [Claude Code](https://claude.ai/code)
-
-Co-Authored-By: Claude <noreply@anthropic.com>
-
-Signed-off-by: phernandez <paul@basicmachines.co>
-
-### Chores
-
-- Remove duplicate code in entity_service.py from bad merge
-  ([`681af5d`](https://github.com/basicmachines-co/basic-memory/commit/681af5d4505dadc40b4086630f739d76bac9201d))
-
-Signed-off-by: phernandez <paul@basicmachines.co>
-
-### Documentation
-
-- Add help docs to mcp cli tools
-  ([`731b502`](https://github.com/basicmachines-co/basic-memory/commit/731b502d36cec253d114403d73b48fab3c47786e))
-
-Signed-off-by: phernandez <paul@basicmachines.co>
-
-- Add mcp badge, update cli reference, llms-install.md
-  ([`b26afa9`](https://github.com/basicmachines-co/basic-memory/commit/b26afa927f98021246cd8b64858e57333595ea90))
-
-Signed-off-by: phernandez <paul@basicmachines.co>
-
-- Update CLAUDE.md ([#33](https://github.com/basicmachines-co/basic-memory/pull/33),
-  [`dfaf0fe`](https://github.com/basicmachines-co/basic-memory/commit/dfaf0fea9cf5b97d169d51a6276ec70162c21a7e))
-
-fix spelling in CLAUDE.md: enviroment -> environment Signed-off-by: Ikko Eltociear Ashimine
-  <eltociear@gmail.com>
-
-### Refactoring
-
-- Move project stats into projct subcommand
-  ([`2a881b1`](https://github.com/basicmachines-co/basic-memory/commit/2a881b1425c73947f037fbe7ac5539c015b62526))
-
-Signed-off-by: phernandez <paul@basicmachines.co>
-
-
-## v0.10.0 (2025-03-15)
-
-### Bug Fixes
-
-- Ai_resource_guide.md path
-  ([`da97353`](https://github.com/basicmachines-co/basic-memory/commit/da97353cfc3acc1ceb0eca22ac6af326f77dc199))
-
-Signed-off-by: phernandez <paul@basicmachines.co>
-
-- Ai_resource_guide.md path
-  ([`c4732a4`](https://github.com/basicmachines-co/basic-memory/commit/c4732a47b37dd2e404139fb283b65556c81ce7c9))
-
-- Ai_resource_guide.md path
-  ([`2e9d673`](https://github.com/basicmachines-co/basic-memory/commit/2e9d673e54ad6a63a971db64f01fc2f4e59c2e69))
-
-Signed-off-by: phernandez <paul@basicmachines.co>
-
-- Don't sync *.tmp files on watch ([#31](https://github.com/basicmachines-co/basic-memory/pull/31),
-  [`6b110b2`](https://github.com/basicmachines-co/basic-memory/commit/6b110b28dd8ba705ebfc0bcb41faf2cb993da2c3))
-
-Fixes #30
-
-Signed-off-by: phernandez <paul@basicmachines.co>
-
-- Drop search_index table on db reindex
-  ([`31cca6f`](https://github.com/basicmachines-co/basic-memory/commit/31cca6f913849a0ab8fc944803533e3072e9ef88))
-
-Signed-off-by: phernandez <paul@basicmachines.co>
-
-- Improve utf-8 support for file reading/writing
-  ([#32](https://github.com/basicmachines-co/basic-memory/pull/32),
-  [`eb5e4ec`](https://github.com/basicmachines-co/basic-memory/commit/eb5e4ec6bd4d2fe757087be030d867f4ca1d38ba))
-
-fixes #29
-
-Signed-off-by: phernandez <paul@basicmachines.co>
-
-### Chores
-
-- Remove logfire
-  ([`9bb8a02`](https://github.com/basicmachines-co/basic-memory/commit/9bb8a020c3425a02cb3a88f6f02adcd281bccee2))
-
-Signed-off-by: phernandez <paul@basicmachines.co>
-
-### Documentation
-
-- Add glama badge. Fix typos in README.md
-  ([#28](https://github.com/basicmachines-co/basic-memory/pull/28),
-  [`9af913d`](https://github.com/basicmachines-co/basic-memory/commit/9af913da4fba7bb4908caa3f15f2db2aa03777ec))
-
-Signed-off-by: phernandez <paul@basicmachines.co>
-
-- Update CLAUDE.md with GitHub integration capabilities
-  ([#25](https://github.com/basicmachines-co/basic-memory/pull/25),
-  [`fea2f40`](https://github.com/basicmachines-co/basic-memory/commit/fea2f40d1b54d0c533e6d7ee7ce1aa7b83ad9a47))
-
-This PR updates the CLAUDE.md file to document the GitHub integration capabilities that enable
-  Claude to participate directly in the development workflow.
-
-### Features
-
-- Add Smithery integration for easier installation
-  ([#24](https://github.com/basicmachines-co/basic-memory/pull/24),
-  [`eb1e7b6`](https://github.com/basicmachines-co/basic-memory/commit/eb1e7b6088b0b3dead9c104ee44174b2baebf417))
-
-This PR adds support for deploying Basic Memory on the Smithery platform.
-
-Signed-off-by: bm-claudeai <claude@basicmachines.co>
-
-
 ## v0.9.0 (2025-03-07)
 
 ### Chores

CLAUDE.md

@@ -37,7 +37,6 @@ See the [README.md](README.md) file for a project overview.
 - API uses FastAPI for endpoints
 - Follow the repository pattern for data access
 - Tools communicate to api routers via the httpx ASGI client (in process)
-- avoid using "private" functions in modules or classes (prepended with _)
 
 ### Codebase Architecture
 
@@ -64,7 +63,7 @@ See the [README.md](README.md) file for a project overview.
 - Testing uses pytest with asyncio support (strict mode)
 - Test database uses in-memory SQLite
 - Avoid creating mocks in tests in most circumstances.
-- Each test runs in a standalone environment with in memory SQLite and tmp_file directory
+- Each test runs in a standalone enviroment with in memory SQLite and tmp_file directory
 
 ## BASIC MEMORY PRODUCT USAGE
 
@@ -107,7 +106,7 @@ See the [README.md](README.md) file for a project overview.
       1d", "1 week")
 
   **Search & Discovery:**
-    - `search_notes(query, page, page_size)` - Full-text search across all content with filtering options
+    - `search(query, page, page_size)` - Full-text search across all content with filtering options
 
   **Visualization:**
     - `canvas(nodes, edges, title, folder)` - Generate Obsidian canvas files for knowledge graph visualization
@@ -115,7 +114,7 @@ See the [README.md](README.md) file for a project overview.
 - MCP Prompts for better AI interaction:
     - `ai_assistant_guide()` - Guidance on effectively using Basic Memory tools for AI assistants
     - `continue_conversation(topic, timeframe)` - Continue previous conversations with relevant historical context
-    - `search_notes(query, after_date)` - Search with detailed, formatted results for better context understanding
+    - `search(query, after_date)` - Search with detailed, formatted results for better context understanding
     - `recent_activity(timeframe)` - View recently changed items with formatted output
     - `json_canvas_spec()` - Full JSON Canvas specification for Obsidian visualization
 
@@ -131,59 +130,4 @@ of using AI just for code generation, we've developed a true collaborative workf
 5. Results improve through iterative collaboration and shared understanding
 
 This approach has allowed us to tackle more complex challenges and build a more robust system than either humans or AI
-could achieve independently.
-
-## GitHub Integration
-
-Basic Memory uses Claude directly into the development workflow through GitHub:
-
-### GitHub MCP Tools
-
-Using the GitHub Model Context Protocol server, Claude can:
-
-- **Repository Management**:
-    - View repository files and structure
-    - Read file contents
-    - Create new branches
-    - Create and update files
-
-- **Issue Management**:
-    - Create new issues
-    - Comment on existing issues
-    - Close and update issues
-    - Search across issues
-
-- **Pull Request Workflow**:
-    - Create pull requests
-    - Review code changes
-    - Add comments to PRs
-
-This integration enables Claude to participate as a full team member in the development process, not just as a code
-generation tool. Claude's GitHub account ([bm-claudeai](https://github.com/bm-claudeai)) is a member of the Basic
-Machines organization with direct contributor access to the codebase.
-
-### Collaborative Development Process
-
-With GitHub integration, the development workflow includes:
-
-1. **Direct code review** - Claude can analyze PRs and provide detailed feedback
-2. **Contribution tracking** - All of Claude's contributions are properly attributed in the Git history
-3. **Branch management** - Claude can create feature branches for implementations
-4. **Documentation maintenance** - Claude can keep documentation updated as the code evolves
-
-With this integration, the AI assistant is a full-fledged team member rather than just a tool for generating code
-snippets.
-
-
-### Basic Memory Pro
-
-Basic Memory Pro is a desktop GUI application that wraps the basic-memory CLI/MCP tools:
-
-- Built with Tauri (Rust), React (TypeScript), and a Python FastAPI sidecar
-- Provides visual knowledge graph exploration and project management
-- Uses the same core codebase but adds a desktop-friendly interface
-- Project configuration is shared between CLI and Pro versions
-- Multiple project support with visual switching interface
-
-local repo: /Users/phernandez/dev/basicmachines/basic-memory-pro
-github: https://github.com/basicmachines-co/basic-memory-pro
+could achieve independently.

CONTRIBUTING.md

@@ -1,7 +1,6 @@
 # Contributing to Basic Memory
 
-Thank you for considering contributing to Basic Memory! This document outlines the process for contributing to the
-project and how to get started as a developer.
+Thank you for considering contributing to Basic Memory! This document outlines the process for contributing to the project and how to get started as a developer.
 
 ## Getting Started
 
@@ -66,64 +65,61 @@ project and how to get started as a developer.
 
 This project is designed for collaborative development between humans and LLMs (Large Language Models):
 
-1. **CLAUDE.md**: The repository includes a `CLAUDE.md` file that serves as a project guide for both humans and LLMs.
-   This file contains:
-    - Key project information and architectural overview
-    - Development commands and workflows
-    - Code style guidelines
-    - Documentation standards
+1. **CLAUDE.md**: The repository includes a `CLAUDE.md` file that serves as a project guide for both humans and LLMs. This file contains:
+   - Key project information and architectural overview
+   - Development commands and workflows
+   - Code style guidelines
+   - Documentation standards
 
 2. **AI-Human Collaborative Workflow**:
-    - We encourage using LLMs like Claude for code generation, reviews, and documentation
-    - When possible, save context in markdown files that can be referenced later
-    - This enables seamless knowledge transfer between different development sessions
-    - Claude can help with implementation details while you focus on architecture and design
+   - We encourage using LLMs like Claude for code generation, reviews, and documentation
+   - When possible, save context in markdown files that can be referenced later
+   - This enables seamless knowledge transfer between different development sessions
+   - Claude can help with implementation details while you focus on architecture and design
 
 3. **Adding to CLAUDE.md**:
-    - If you discover useful project information or common commands, consider adding them to CLAUDE.md
-    - This helps all contributors (human and AI) maintain consistent knowledge of the project
+   - If you discover useful project information or common commands, consider adding them to CLAUDE.md
+   - This helps all contributors (human and AI) maintain consistent knowledge of the project
 
 ## Pull Request Process
 
 1. **Create a Pull Request**: Open a PR against the `main` branch with a clear title and description.
-2. **Sign the Developer Certificate of Origin (DCO)**: All contributions require signing our DCO, which certifies that
-   you have the right to submit your contributions. This will be automatically checked by our CLA assistant when you
-   create a PR.
+2. **Sign the Developer Certificate of Origin (DCO)**: All contributions require signing our DCO, which certifies that you have the right to submit your contributions. This will be automatically checked by our CLA assistant when you create a PR.
 3. **PR Description**: Include:
-    - What the PR changes
-    - Why the change is needed
-    - How you tested the changes
-    - Any related issues (use "Fixes #123" to automatically close issues)
+   - What the PR changes
+   - Why the change is needed
+   - How you tested the changes
+   - Any related issues (use "Fixes #123" to automatically close issues)
 4. **Code Review**: Wait for code review and address any feedback.
 5. **CI Checks**: Ensure all CI checks pass.
 6. **Merge**: Once approved, a maintainer will merge your PR.
 
 ## Developer Certificate of Origin
 
-By contributing to this project, you agree to the [Developer Certificate of Origin (DCO)](CLA.md). This means you
-certify that:
-
+By contributing to this project, you agree to the [Developer Certificate of Origin (DCO)](CLA.md). This means you certify that:
 - You have the right to submit your contributions
 - You're not knowingly submitting code with patent or copyright issues
 - Your contributions are provided under the project's license (AGPL-3.0)
 
-This is a lightweight alternative to a Contributor License Agreement and helps ensure that all contributions can be
-properly incorporated into the project and potentially used in commercial applications.
+This is a lightweight alternative to a Contributor License Agreement and helps ensure that all contributions can be properly incorporated into the project and potentially used in commercial applications.
 
 ### Signing Your Commits
 
-Sign your commit:
+You can sign your commits in one of two ways:
 
-**Using the `-s` or `--signoff` flag**:
+1. **Using the `-s` or `--signoff` flag**:
+   ```bash
+   git commit -s -m "Your commit message"
+   ```
+   This adds a `Signed-off-by` line to your commit message, certifying that you adhere to the DCO.
 
-```bash
-git commit -s -m "Your commit message"
-```
+2. **Configuring Git to automatically sign off**:
+   ```bash
+   git config --global alias.cs 'commit -s'
+   ```
+   Then use `git cs -m "Your commit message"` to commit with sign-off.
 
-This adds a `Signed-off-by` line to your commit message, certifying that you adhere to the DCO.
-
-The sign-off certifies that you have the right to submit your contribution under the project's license and verifies your
-agreement to the DCO.
+The sign-off certifies that you have the right to submit your contribution under the project's license and verifies your agreement to the DCO.
 
 ## Code Style Guidelines
 
@@ -139,10 +135,10 @@ agreement to the DCO.
 
 - **Coverage Target**: We aim for 100% test coverage for all code
 - **Test Framework**: Use pytest for unit and integration tests
-- **Mocking**: Use pytest-mock for mocking dependencies only when necessary
+- **Mocking**: Use pytest-mock for mocking dependencies
 - **Edge Cases**: Test both normal operation and edge cases
 - **Database Testing**: Use in-memory SQLite for testing database operations
-- **Fixtures**: Use async pytest fixtures for setup and teardown
+- **Fixtures**: Use pytest fixtures for setup and teardown
 
 ## Creating Issues
 
@@ -160,4 +156,4 @@ All contributors must follow the [Code of Conduct](CODE_OF_CONDUCT.md).
 
 ## Thank You!
 
-Your contributions help make Basic Memory better. We appreciate your time and effort!
+Your contributions help make Basic Memory better for everyone. We appreciate your time and effort!

Dockerfile

@@ -8,9 +8,9 @@ COPY . .
 
 # Install pip and build dependencies
 RUN pip install --upgrade pip \
-&& pip install . --no-cache-dir --ignore-installed
+    && pip install . --no-cache-dir --ignore-installed
 
 # Expose port if necessary (e.g., uv might use a port, but MCP over stdio so not needed here)
 
 # Use the basic-memory entrypoint to run the MCP server
-CMD ["basic-memory", "mcp"]
+CMD ["basic-memory", "mcp"]

README.md

@@ -1,34 +1,39 @@
+# Basic Memory
+
 [![License: AGPL v3](https://img.shields.io/badge/License-AGPL_v3-blue.svg)](https://www.gnu.org/licenses/agpl-3.0)
 [![PyPI version](https://badge.fury.io/py/basic-memory.svg)](https://badge.fury.io/py/basic-memory)
 [![Python 3.12+](https://img.shields.io/badge/python-3.12+-blue.svg)](https://www.python.org/downloads/)
 [![Tests](https://github.com/basicmachines-co/basic-memory/workflows/Tests/badge.svg)](https://github.com/basicmachines-co/basic-memory/actions)
 [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
-![](https://badge.mcpx.dev?type=server 'MCP Server')
-![](https://badge.mcpx.dev?type=dev 'MCP Dev')
 [![smithery badge](https://smithery.ai/badge/@basicmachines-co/basic-memory)](https://smithery.ai/server/@basicmachines-co/basic-memory)
 
-# Basic Memory
-
 Basic Memory lets you build persistent knowledge through natural conversations with Large Language Models (LLMs) like
 Claude, while keeping everything in simple Markdown files on your computer. It uses the Model Context Protocol (MCP) to
 enable any compatible LLM to read and write to your local knowledge base.
 
-- Website: https://basicmachines.co
-- Documentation: https://memory.basicmachines.co
+- Website: http://basicmachines.co
+- Documentation: http://memory.basicmachines.co
 
-## Pick up your conversation right where you left off
+![Example Gif](docs/attachments/Obsidian-CoffeeKnowledgeBase-examples-overlays.gif)
 
-- AI assistants can load context from local files in a new conversation
-- Notes are saved locally as Markdown files in real time
-- No project knowledge or special prompting required
-
-https://github.com/user-attachments/assets/a55d8238-8dd0-454a-be4c-8860dbbd0ddc
+Basic Memory provides persistent contextual awareness across sessions through a structured knowledge graph.
+The system enables LLMs to access and reference prior conversations, track semantic relationships between concepts, and
+incorporate human edits made directly to knowledge files.
 
 ## Quick Start
 
+### Installing via Smithery
+
+To install Basic Memory for Claude Desktop automatically via [Smithery](https://smithery.ai/server/@basicmachines-co/basic-memory):
+
+```bash
+npx -y @smithery/cli install @basicmachines-co/basic-memory --client claude
+```
+
+### Installing Manually
 ```bash
 # Install with uv (recommended)
-uv tool install basic-memory
+uv install basic-memory
 
 # Configure Claude Desktop (edit ~/Library/Application Support/Claude/claude_desktop_config.json)
 # Add this to your config:
@@ -52,23 +57,33 @@ uv tool install basic-memory
 
 You can view shared context via files in `~/basic-memory` (default directory location).
 
-### Alternative Installation via Smithery
+You can also install the cli tools to sync files or manage projects.
 
-You can use [Smithery](https://smithery.ai/server/@basicmachines-co/basic-memory) to automatically configure Basic
-Memory for Claude Desktop:
+```bash 
+uv tool install basic-memory
 
-```bash
-npx -y @smithery/cli install @basicmachines-co/basic-memory --client claude
+# create a new project in a different directory
+basic-memory project add coffee ./examples/coffee
+
+# you can set the project to the default 
+basic-memory project default coffee
 ```
 
-This installs and configures Basic Memory without requiring manual edits to the Claude Desktop configuration file. The
-Smithery server hosts the MCP server component, while your data remains stored locally as Markdown files.
+View available projects
 
-### Glama.ai
+```bash 
+basic-memory project list
+                             Basic Memory Projects
+┏━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━┓
+┃ Name   ┃ Path                                             ┃ Default ┃ Active ┃
+┡━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━╇━━━━━━━━┩
+│ main   │ ~/basic-memory                                   │ ✓       │ ✓      │
+│ coffee │ ~/dev/basicmachines/basic-memory/examples/coffee │         │        │
+└────────┴──────────────────────────────────────────────────┴─────────┴────────┘
+```
 
-<a href="https://glama.ai/mcp/servers/o90kttu9ym">
-  <img width="380" height="200" src="https://glama.ai/mcp/servers/o90kttu9ym/badge" alt="basic-memory MCP server" />
-</a>
+Basic Memory will write notes in Markdown format. Open you project directory in your text editor to view project files
+while you have conversations with an LLM.
 
 ## Why Basic Memory?
 
@@ -149,13 +164,36 @@ tags:
 - affects [[Flavor Extraction]]
 ```
 
-The note embeds semantic content and links to other topics via simple Markdown formatting.
+The note embeds semantic content and links to other topics via simple Markdown
+formatting.
 
-3. You see this file on your computer in real time in the current project directory (default `~/$HOME/basic-memory`).
+3. You see this file on your computer in real time in the `~/$HOME/basic-memory` directory:
 
-- Realtime sync is enabled by default with the v0.12.0 version
+```markdown
+---
+title: Coffee Brewing Methods
+permalink: coffee-brewing-methods
+type: note
+---
 
-4. In a chat with the LLM, you can reference a topic:
+# Coffee Brewing Methods
+
+## Observations
+
+- [method] Pour over provides more clarity and highlights subtle flavors
+- [technique] Water temperature at 205°F (96°C) extracts optimal compounds
+- [principle] Freshly ground beans preserve aromatics and flavor
+- [preference] Medium-light roasts work best for pour over # Added by you
+
+## Relations
+
+- relates_to [[Coffee Bean Origins]]
+- requires [[Proper Grinding Technique]]
+- affects [[Flavor Extraction]]
+- pairs_with [[Breakfast Pastries]]  # Added by you
+```
+
+4. In a new chat with the LLM, you can reference this knowledge:
 
 ```
 Look at `coffee-brewing-methods` for context about pour over coffee
@@ -175,14 +213,15 @@ Following relation 'requires [[Proper Grinding Technique]]':
 - Impact of consistent particle size on extraction
 ```
 
-Each related document can lead to more context, building a rich semantic understanding of your knowledge base.
+Each related document can lead to more context, building a rich semantic understanding of your knowledge base. All of
+this context comes from standard Markdown files that both humans and LLMs can read and write.
 
-This creates a two-way flow where:
+Every time the LLM writes notes,they are saved in local Markdown files that you can:
 
-- Humans write and edit Markdown files
-- LLMs read and write through the MCP protocol
-- Sync keeps everything consistent
-- All knowledge stays in local files.
+- Edit in any text editor
+- Version via git
+- Back up normally
+- Share when you want to
 
 ## Technical Implementation
 
@@ -218,7 +257,7 @@ permalink: <a uri slug>
 
 Observations are facts about a topic.
 They can be added by creating a Markdown list with a special format that can reference a `category`, `tags` using a
-"#" character, and an optional `context`.
+"#" charactor, and an optional `context`.
 
 Observation Markdown format:
 
@@ -262,42 +301,72 @@ Examples of relations:
 - documented_in [[Coffee Journal]]
 ```
 
-## Using with VS Code
-For one-click installation, click one of the install buttons below...
+### Complete Example
 
-[![Install with UV in VS Code](https://img.shields.io/badge/VS_Code-UV-0098FF?style=flat-square&logo=visualstudiocode&logoColor=white)](https://insiders.vscode.dev/redirect/mcp/install?name=basic-memory&config=%7B%22command%22%3A%22uvx%22%2C%22args%22%3A%5B%22basic-memory%22%2C%22mcp%22%5D%7D) [![Install with UV in VS Code Insiders](https://img.shields.io/badge/VS_Code_Insiders-UV-24bfa5?style=flat-square&logo=visualstudiocode&logoColor=white)](https://insiders.vscode.dev/redirect/mcp/install?name=basic-memory&config=%7B%22command%22%3A%22uvx%22%2C%22args%22%3A%5B%22basic-memory%22%2C%22mcp%22%5D%7D&quality=insiders)
+Here's a complete example of a note with frontmatter, observations, and relations:
 
-You can use Basic Memory with VS Code to easily retrieve and store information while coding. Click the installation buttons above for one-click setup, or follow the manual installation instructions below.
+```markdown
+---
+title: Pour Over Coffee Method
+type: note
+permalink: pour-over-coffee-method
+tags:
+- brewing
+- coffee
+- techniques
+---
 
-### Manual Installation
+# Pour Over Coffee Method
 
-Add the following JSON block to your User Settings (JSON) file in VS Code. You can do this by pressing `Ctrl + Shift + P` and typing `Preferences: Open User Settings (JSON)`.
+This note documents the pour over brewing method and my experiences with it.
 
-```json
-{
-  "mcp": {
-    "servers": {
-      "basic-memory": {
-        "command": "uvx",
-        "args": ["basic-memory", "mcp"]
-      }
-    }
-  }
-}
+## Overview
+
+The pour over method involves pouring hot water through coffee grounds in a filter. The water drains through the coffee
+and filter into a carafe or cup.
+
+## Observations
+
+- [equipment] Hario V60 dripper produces clean, bright cup #gear
+- [technique] Pour in concentric circles to ensure even extraction
+- [ratio] 1:16 coffee-to-water ratio works best for balanced flavor
+- [timing] Total brew time should be 2:30-3:00 minutes for medium roast
+- [temperature] Water at 205°F (96°C) extracts optimal flavor compounds
+- [grind] Medium-fine grind similar to table salt texture
+- [tip] 30-45 second bloom with double the coffee weight in water
+- [result] Produces a cleaner cup with more distinct flavor notes than immersion methods
+
+## Relations
+
+- complements [[Light Roast Beans]]
+- requires [[Gooseneck Kettle]]
+- contrasts_with [[French Press Method]]
+- pairs_with [[Breakfast Pastries]]
+- documented_in [[Brewing Journal]]
+- inspired_by [[Japanese Brewing Techniques]]
+- affects [[Flavor Extraction]]
+- part_of [[Morning Ritual]]
 ```
 
-Optionally, you can add it to a file called `.vscode/mcp.json` in your workspace. This will allow you to share the configuration with others.
+Basic Memory will parse the Markdown and derive the semantic relationships in the content. When you run
+`basic-memory sync`:
 
-```json
-{
-  "servers": {
-    "basic-memory": {
-      "command": "uvx",
-      "args": ["basic-memory", "mcp"]
-    }
-  }
-}
-```
+1. New and changed files are detected
+2. Markdown patterns become semantic knowledge:
+
+- `[tech]` becomes a categorized observation
+- `[[WikiLink]]` creates a relation in the knowledge graph
+- Tags and metadata are indexed for search
+
+3. A SQLite database maintains these relationships for fast querying
+4. MCP-compatible LLMs can access this knowledge via memory:// URLs
+
+This creates a two-way flow where:
+
+- Humans write and edit Markdown files
+- LLMs read and write through the MCP protocol
+- Sync keeps everything consistent
+- All knowledge stays in local files.
 
 ## Using with Claude Desktop
 
@@ -322,8 +391,7 @@ for OS X):
 }
 ```
 
-If you want to use a specific project (see [Multiple Projects](docs/User%20Guide.md#multiple-projects)), update your
-Claude Desktop
+If you want to use a specific project (see [Multiple Projects](#multiple-projects) below), update your Claude Desktop
 config:
 
 ```json
@@ -333,9 +401,9 @@ config:
       "command": "uvx",
       "args": [
         "basic-memory",
+        "mcp",
         "--project",
-        "your-project-name",
-        "mcp"
+        "your-project-name"
       ]
     }
   }
@@ -344,7 +412,13 @@ config:
 
 2. Sync your knowledge:
 
-Basic Memory will sync the files in your project in real time if you make manual edits.
+```bash
+# One-time sync of local knowledge updates
+basic-memory sync
+
+# Run realtime sync process (recommended)
+basic-memory sync --watch
+```
 
 3. In Claude Desktop, the LLM can now use these tools:
 
@@ -352,7 +426,7 @@ Basic Memory will sync the files in your project in real time if you make manual
 write_note(title, content, folder, tags) - Create or update notes
 read_note(identifier, page, page_size) - Read notes by title or permalink
 build_context(url, depth, timeframe) - Navigate knowledge graph via memory:// URLs
-search_notes(query, page, page_size) - Search across your knowledge base
+search(query, page, page_size) - Search across your knowledge base
 recent_activity(type, depth, timeframe) - Find recently updated information
 canvas(nodes, edges, title, folder) - Generate knowledge visualizations
 ```
@@ -367,30 +441,263 @@ canvas(nodes, edges, title, folder) - Generate knowledge visualizations
 "What have I been working on in the past week?"
 ```
 
-## Futher info
+## Multiple Projects
 
-See the [Documentation](https://memory.basicmachines.co/) for more info, including:
+Basic Memory supports managing multiple separate knowledge bases through projects. This feature allows you to maintain
+separate knowledge graphs for different purposes (e.g., personal notes, work projects, research topics).
 
-- [Complete User Guide](https://memory.basicmachines.co/docs/user-guide)
-- [CLI tools](https://memory.basicmachines.co/docs/cli-reference)
-- [Managing multiple Projects](https://memory.basicmachines.co/docs/cli-reference#project)
-- [Importing data from OpenAI/Claude Projects](https://memory.basicmachines.co/docs/cli-reference#import)
+### Managing Projects
+
+```bash
+# List all configured projects
+basic-memory project list
+
+# Add a new project
+basic-memory project add work ~/work-basic-memory
+
+# Set the default project
+basic-memory project default work
+
+# Remove a project (doesn't delete files)
+basic-memory project remove personal
+
+# Show current project
+basic-memory project current
+```
+
+### Using Projects in Commands
+
+All commands support the `--project` flag to specify which project to use:
+
+```bash
+# Sync a specific project
+basic-memory --project=work sync
+
+# Run MCP server for a specific project
+basic-memory --project=personal mcp
+```
+
+You can also set the `BASIC_MEMORY_PROJECT` environment variable:
+
+```bash
+BASIC_MEMORY_PROJECT=work basic-memory sync
+```
+
+### Project Isolation
+
+Each project maintains:
+
+- Its own collection of markdown files in the specified directory
+- A separate SQLite database for that project
+- Complete knowledge graph isolation from other projects
+
+## Design Philosophy
+
+Basic Memory is built on some key ideas:
+
+- Your knowledge should stay in files you control
+- Both humans and AI should use natural formats
+- Simple text patterns can capture rich meaning
+- Local-first doesn't mean feature-poor
+- Knowledge should persist across conversations
+- AI assistants should build on past context
+- File formats should be human-readable and editable
+- Semantic structure should emerge from natural patterns
+- Knowledge graphs should be both AI and human navigable
+- Systems should augment human memory, not replace it
+
+## Importing Existing Data
+
+Basic Memory provides CLI commands to import data from various sources, converting them into the structured Markdown
+format:
+
+### Claude.ai
+
+First, request an export of your data from your Claude account. The data will be emailed to you in several files,
+including
+`conversations.json` and `projects.json`.
+
+Import Claude.ai conversation data
+
+```bash
+ basic-memory import claude conversations 
+```
+
+The conversations will be turned into Markdown files and placed in the "conversations" folder by default (this can be
+changed with the --folder arg).
+
+Example:
+
+```bash
+Importing chats from conversations.json...writing to .../basic-memory
+  Reading chat data... ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100%
+╭────────────────────────────╮
+│ Import complete!           │
+│                            │
+│ Imported 307 conversations │
+│ Containing 7769 messages   │
+╰────────────────────────────╯
+```
+
+Next, you can run the `sync` command to import the data into basic-memory
+
+```bash
+basic-memory sync
+```
+
+You can also import project data from Claude.ai
+
+```bash 
+➜  basic-memory import claude projects
+Importing projects from projects.json...writing to .../basic-memory/projects
+  Reading project data... ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100%
+╭────────────────────────────────╮
+│ Import complete!               │
+│                                │
+│ Imported 101 project documents │
+│ Imported 32 prompt templates   │
+╰────────────────────────────────╯
+
+Run 'basic-memory sync' to index the new files.
+```
+
+### OpenAI ChatGPT
+
+```bash
+ ➜  basic-memory import chatgpt
+Importing chats from conversations.json...writing to .../basic-memory/conversations
+
+  Reading chat data... ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100%
+╭────────────────────────────╮
+│ Import complete!           │
+│                            │
+│ Imported 198 conversations │
+│ Containing 11777 messages  │
+╰────────────────────────────╯
+
+
+```
+
+### Knowledge Graph Memory Server
+
+From the MCP Server: https://github.com/modelcontextprotocol/servers/tree/main/src/memory
+
+```bash
+➜  basic-memory import memory-json
+Importing from memory.json...writing to .../basic-memory
+  Reading memory.json... ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100%
+  Creating entities...   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100%
+╭──────────────────────╮
+│ Import complete!     │
+│                      │
+│ Created 126 entities │
+│ Added 252 relations  │
+╰──────────────────────╯
+```
+
+## Working with Your Knowledge Base
+
+Once you've built up a knowledge base, you can interact with it in several ways:
+
+### Command Line Interface
+
+Basic Memory provides a powerful CLI for managing your knowledge:
+
+```bash
+# See all available commands
+basic-memory --help
+
+# Check the status of your knowledge sync
+basic-memory status
+
+# Access specific tool functionality directly
+basic-memory tools
+
+# Start a continuous sync process
+basic-memory sync --watch
+```
+
+### Obsidian Integration
+
+Basic Memory works seamlessly with [Obsidian](https://obsidian.md/), a popular knowledge management app:
+
+1. Point Obsidian to your Basic Memory directory
+2. Use standard Obsidian features like backlinks and graph view
+3. See your knowledge graph visually
+4. Use the canvas visualization generated by Basic Memory
+
+### File Organization
+
+Basic Memory is flexible about how you organize your files:
+
+- Group by topic in folders
+- Use a flat structure with descriptive filenames
+- Add custom metadata in frontmatter
+- Tag files for better searchability
+
+The system will build the semantic knowledge graph regardless of your file organization preference.
+
+## Using stdin with Basic Memory's `write_note` Tool
+
+The `write-note` tool supports reading content from standard input (stdin), allowing for more flexible workflows when
+creating or updating notes in your Basic Memory knowledge base.
+
+### Use Cases
+
+This feature is particularly useful for:
+
+1. **Piping output from other commands** directly into Basic Memory notes
+2. **Creating notes with multi-line content** without having to escape quotes or special characters
+3. **Integrating with AI assistants** like Claude Code that can generate content and pipe it to Basic Memory
+4. **Processing text data** from files or other sources
+
+## Basic Usage
+
+### Method 1: Using a Pipe
+
+You can pipe content from another command into `write_note`:
+
+```bash
+# Pipe output of a command into a new note
+echo "# My Note\n\nThis is a test note" | basic-memory tools write-note --title "Test Note" --folder "notes"
+
+# Pipe output of a file into a new note
+cat README.md | basic-memory tools write-note --title "Project README" --folder "documentation"
+
+# Process text through other tools before saving as a note
+cat data.txt | grep "important" | basic-memory tools write-note --title "Important Data" --folder "data"
+```
+
+### Method 2: Using Heredoc Syntax
+
+For multi-line content, you can use heredoc syntax:
+
+```bash
+# Create a note with heredoc
+cat << EOF | basic-memory tools write_note --title "Project Ideas" --folder "projects"
+# Project Ideas for Q2
+
+## AI Integration
+- Improve recommendation engine
+- Add semantic search to product catalog
+
+## Infrastructure
+- Migrate to Kubernetes
+- Implement CI/CD pipeline
+EOF
+```
+
+### Method 3: Input Redirection
+
+You can redirect input from a file:
+
+```bash
+# Create a note from file content
+basic-memory tools write-note --title "Meeting Notes" --folder "meetings" < meeting_notes.md
+```
 
 ## License
 
 AGPL-3.0
 
-Contributions are welcome. See the [Contributing](CONTRIBUTING.md) guide for info about setting up the project locally
-and submitting PRs.
-
-## Star History
-
-<a href="https://www.star-history.com/#basicmachines-co/basic-memory&Date">
- <picture>
-   <source media="(prefers-color-scheme: dark)" srcset="https://api.star-history.com/svg?repos=basicmachines-co/basic-memory&type=Date&theme=dark" />
-   <source media="(prefers-color-scheme: light)" srcset="https://api.star-history.com/svg?repos=basicmachines-co/basic-memory&type=Date" />
-   <img alt="Star History Chart" src="https://api.star-history.com/svg?repos=basicmachines-co/basic-memory&type=Date" />
- </picture>
-</a>
-
 Built with ♥️ by Basic Machines

SECURITY.md

@@ -1,13 +0,0 @@
-# Security Policy
-
-## Supported Versions
-
-| Version | Supported          |
-| ------- | ------------------ |
-| 0.x.x   | :white_check_mark: |
-
-## Reporting a Vulnerability
-
-Use this section to tell people how to report a vulnerability.
-
-If you find a vulnerability, please contact hello@basicmachines.co

claude-output/claude_issue_fix_log_75.txt

@@ -1,13 +0,0 @@
-Starting issue-fix mode at Sat Apr  5 18:02:54 UTC 2025
-Fetching issue #75 details
-Using repository: basicmachines-co/basic-memory
-Checking if phernandez is a member of organization basicmachines-co
-User phernandez is a member of organization basicmachines-co. Proceeding with Claude fix.
-Creating a new branch: fix-issue-75-20250405180254
-From https://github.com/basicmachines-co/basic-memory
- * branch            main       -> FETCH_HEAD
-Switched to a new branch 'fix-issue-75-20250405180254'
-branch 'fix-issue-75-20250405180254' set up to track 'origin/main'.
-Prompt saved to ./claude-output/claude_prompt_75.txt for debugging
-Running Claude to fix the issue...
-Committing changes...

claude-output/claude_output_75.txt

@@ -1,35 +0,0 @@
-Let's summarize the changes we've made to fix issue #75:
-
-1. We updated the `search_notes` tool in `/src/basic_memory/mcp/tools/search.py` to accept primitive types as parameters instead of a complex Pydantic `SearchQuery` object. This makes it easier for LLMs like Cursor to make proper tool calls.
-
-2. We converted the internal implementation to create a SearchQuery object from the primitive parameters, maintaining backward compatibility with the existing API.
-
-3. We updated tests in `/tests/mcp/test_tool_search.py` to use the new function signature with primitive parameters.
-
-4. We updated code in `/src/basic_memory/mcp/tools/read_note.py` to use the new function signature when making calls to `search_notes`.
-
-5. We updated code in `/src/basic_memory/mcp/prompts/search.py` to use the new function signature when making calls to `search_notes`.
-
-These changes should make it easier for Cursor and other LLMs to use the search_notes tool by eliminating the complex Pydantic object parameter in favor of simple primitive parameters.
-
----SUMMARY---
-Fixed issue #75 where Cursor was having errors calling the search_notes tool. The problem was that the search_notes tool was expecting a complex Pydantic object (SearchQuery) as input, which was confusing Cursor. 
-
-Changes:
-1. Modified the search_notes tool to accept primitive types (strings, lists, etc.) as parameters instead of a complex Pydantic object
-2. Updated the implementation to create a SearchQuery object internally from these primitive parameters
-3. Updated all call sites in the codebase that were using the old function signature
-4. Updated tests to use the new function signature
-
-The fix makes it easier for LLMs like Cursor to make proper calls to the search_notes tool, which will resolve the reported error messages:
-- "Parameter 'query' must be of type undefined, got object"
-- "Parameter 'query' must be of type undefined, got string"
-- "Invalid type for parameter 'query' in tool search_notes"
-
-Files modified:
-- src/basic_memory/mcp/tools/search.py
-- src/basic_memory/mcp/tools/read_note.py
-- src/basic_memory/mcp/prompts/search.py
-- tests/mcp/test_tool_search.py
-- tests/mcp/test_tool_read_note.py
----END SUMMARY---

claude-output/claude_prompt_75.txt

@@ -1,49 +0,0 @@
-You are Claude, an AI assistant tasked with fixing issues in a GitHub repository.
-
-Issue #75: [BUG] Cursor has errors calling search tool
-
-Issue Description:
-## Bug Description
-
-
-
-> Cursor cannot figure out how to structure the parameters for that tool call.  No matter what Cursor seems to try it gets the errors.
-> 
-> ```Looking at the error messages more carefully:
-> - When I pass an object: "Parameter 'query' must be of type undefined, got object"
-> - When I pass a string: "Parameter 'query' must be of type undefined, got string"
-> 
-> 
-> 
->  and then it reports:  "Invalid type for parameter 'query' in tool search_notes"
-> Any chance you can give me some guidance with this?
-> 
-
-## Steps To Reproduce
-Steps to reproduce the behavior:
-
-try using search tool in Cursor. 
-
-## Possible Solution
-
-The tool args should probably be plain text and not json to make it easier to call. 
-Additional Instructions from User Comment:
- let make a PR to implement option #1.  
-Your task is to:
-1. Analyze the issue carefully to understand the problem
-2. Look through the repository to identify the relevant files that need to be modified
-3. Make precise changes to fix the issue
-4. Use the Edit tool to modify files directly when needed
-5. Be minimal in your changes - only modify what's necessary to fix the issue
-
-After making changes, provide a summary of what you did in this format:
-
----SUMMARY---
-[Your detailed summary of changes, including which files were modified and how]
----END SUMMARY---
-
-Remember:
-- Be specific in your changes
-- Only modify files that are necessary to fix the issue
-- Follow existing code style and conventions
-- Make the minimal changes needed to resolve the issue

docs/.obsidian/appearance.json

@@ -0,0 +1 @@
+{}

docs/.obsidian/core-plugins.json

@@ -0,0 +1,31 @@
+{
+  "file-explorer": true,
+  "global-search": true,
+  "switcher": true,
+  "graph": true,
+  "backlink": true,
+  "canvas": true,
+  "outgoing-link": true,
+  "tag-pane": true,
+  "properties": false,
+  "page-preview": true,
+  "daily-notes": true,
+  "templates": true,
+  "note-composer": true,
+  "command-palette": true,
+  "slash-command": false,
+  "editor-status": true,
+  "bookmarks": true,
+  "markdown-importer": false,
+  "zk-prefixer": false,
+  "random-note": false,
+  "outline": true,
+  "word-count": true,
+  "slides": false,
+  "audio-recorder": false,
+  "workspaces": false,
+  "file-recovery": true,
+  "publish": true,
+  "sync": true,
+  "webviewer": false
+}

docs/.obsidian/publish.json

@@ -0,0 +1,6 @@
+{
+  "siteId": "947ee055a8c6f1a57efa4afa09791e62",
+  "host": "publish-01.obsidian.md",
+  "included": [],
+  "excluded": []
+}

docs/AI Assistant Guide.md

@@ -4,8 +4,6 @@ type: note
 permalink: docs/ai-assistant-guide
 ---
 > Note: This is an optional document that can be copy/pasted into the project knowledge for an LLM to provide a full description of how it can work with Basic Memory. It is provided as a helpful resource. The tools contain extensive usage description prompts with enable the LLM to understand them. 
-
-You can [download](https://github.com/basicmachines-co/basic-memory/blob/main/docs/AI%20Assistant%20Guide.md) the contents of this file from GitHub
 # AI Assistant Guide for Basic Memory
 
 This guide helps you, the AI assistant, use Basic Memory tools effectively when working with users. It covers reading, writing, and navigating knowledge through the Model Context Protocol (MCP).
@@ -53,7 +51,7 @@ content = await read_note("specs/search-design")       # By path
 content = await read_note("memory://specs/search")     # By memory URL
 
 # Searching for knowledge
-results = await search_notes(
+results = await search(
     query="authentication system",      # Text to search for
     page=1,                             # Optional: Pagination
     page_size=10                        # Optional: Results per page
@@ -154,7 +152,7 @@ Users will interact with Basic Memory in patterns like:
    Human: "What were our decisions about auth?"
    
    You: Let me find that information for you.
-   [Use search_notes() to find relevant notes]
+   [Use search() to find relevant notes]
    [Then build_context() to understand connections]
    ```
 
@@ -251,7 +249,7 @@ When creating relations, you can:
 # Example workflow for creating notes with effective relations
 async def create_note_with_effective_relations():
     # Search for existing entities to reference
-    search_results = await search_notes("travel")
+    search_results = await search("travel")
     existing_entities = [result.title for result in search_results.primary_results]
     
     # Check if specific entities exist
@@ -323,7 +321,7 @@ Common issues to watch for:
        content = await read_note("Document")
    except:
        # Try search instead
-       results = await search_notes("Document")
+       results = await search("Document")
        if results and results.primary_results:
            # Found something similar
            content = await read_note(results.primary_results[0].permalink)
@@ -369,7 +367,7 @@ Common issues to watch for:
    - **Create deliberate relations**: Connect each note to at least 2-3 related entities
    - **Use existing entities**: Before creating a new relation, search for existing entities
    - **Verify wikilinks**: When referencing `[[Entity]]`, use exact titles of existing notes
-   - **Check accuracy**: Use `search_notes()` or `recent_activity()` to confirm entity titles
+   - **Check accuracy**: Use `search()` or `recent_activity()` to confirm entity titles
    - **Use precise relation types**: Choose specific relation types that convey meaning (e.g., "implements" instead of "relates_to")
    - **Consider bidirectional relations**: When appropriate, create inverse relations in both entities
 

docs/CLI Reference.md

@@ -21,30 +21,15 @@ basic-memory sync
 # Watch for changes
 basic-memory sync --watch
 
-# Show detailed sync information
-basic-memory sync --verbose
+# Sync specific folder
+basic-memory sync path/to/folder
 ```
 
 Options:
 - `--watch`: Continuously monitor for changes
 - `--verbose`: Show detailed output
+- `PATH`: Optional path to sync (defaults to ~/basic-memory)
 
-**Note**:
-
-As of the v0.12.0 release syncing will occur in real time when the mcp process starts.
-- The real time sync means that it is no longer necessary to run the `basic-memory sync --watch` process in a a terminal to sync changes to the db (so the AI can see them). This will be done automatically.
-
-This behavior can be changed via the config. The config file for Basic Memory is in the home directory under `.basic-memory/config.json`.
-
-To change the properties, set the following values:
-```
- ~/.basic-memory/config.json 
-{
-  "sync_changes": false,
-}
-```
-
-Thanks for using Basic Memory!
 ### import
 
 Imports external knowledge sources:
@@ -58,13 +43,13 @@ basic-memory import claude projects
 
 # ChatGPT history
 basic-memory import chatgpt
-
-# ChatGPT history
-basic-memory import memory-json /path/to/memory.json
-
 ```
 
-> **Note**: After importing, run `basic-memory sync` to index the new files.
+Options:
+- `--folder PATH`: Target folder for imported content
+- `--overwrite`: Replace existing files
+- `--skip-existing`: Keep existing files
+
 ### status
 
 Shows system status information:
@@ -257,12 +242,10 @@ You can redirect input from a file:
 basic-memory tool write-note --title "Meeting Notes" --folder "meetings" < meeting_notes.md
 ```
 
-## Integration with Claude Code
+#### Integration with Claude Code
 
 This feature works well with Claude Code in the terminal:
 
-### cli
-
 In a Claude Code session, let Claude know he can use the basic-memory tools, then he can execute them via the cli:
 
 ```
@@ -275,32 +258,6 @@ In a Claude Code session, let Claude know he can use the basic-memory tools, the
 
 ```
 
-### MCP
-
-Claude code can also now use mcp tools, so it can use any of the basic-memory tool natively. To install basic-memory in Claude Code:
-
-Run
-```
-claude mcp add basic-memory basic-memory mcp
-```
-
-For example: 
-
-```
-➜  ~ claude mcp add basic-memory basic-memory mcp
-Added stdio MCP server basic-memory with command: basic-memory mcp to project config
-➜  ~ claude mcp list
-basic-memory: basic-memory mcp
-```
-
-You can then use the `/mcp` command in the REPL:
-
-```
-/mcp
-  ⎿  MCP Server Status
-
-     • basic-memory: connected
-```
 
 ## Troubleshooting Common Issues
 

docs/Getting Started with Basic Memory.md

@@ -9,20 +9,15 @@ permalink: docs/getting-started
 This guide will help you install Basic Memory, configure it with Claude Desktop, and create your first knowledge notes
 through conversations.
 
-Basic Memory uses the [Model Context Protocol](https://modelcontextprotocol.io/introduction) (MCP) to connect with LLMs.
-It can be used with any service that supports the MCP, but Claude Desktop works especially well.
+Basic Memory uses the [Model Context Protocol](https://modelcontextprotocol.io/introduction) (MCP) to connect with LLMs. It can be used with any service that supports the MCP, but Claude Desktop works especially well. 
 
 ## Installation
 
-### Prerequisites
-
-The easiest way to install basic memory is via `uv`. See the [uv installation guide](https://docs.astral.sh/uv/getting-started/installation/).
-
 ### 1. Install Basic Memory
 
 ```bash
-# Install with uv (recommended).  
-uv tool install basic-memory
+# Install with uv (recommended)
+uv install basic-memory
 
 # Or with pip
 pip install basic-memory
@@ -30,44 +25,21 @@ pip install basic-memory
 
 > **Important**: You need to install Basic Memory using one of the commands above to use the command line tools.
 
-Using `uv tool install` will install the basic-memory package in a standalone virtual environment. See the [UV docs](https://docs.astral.sh/uv/concepts/tools/) for more info.
-
 ### 2. Configure Claude Desktop
 
-Edit your Claude Desktop config, located at `~/Library/Application Support/Claude/claude_desktop_config.json`:
+Claude Desktop often has trouble finding executables in your user path. Follow these steps for a reliable setup:
 
-```json
-{
-  "mcpServers": {
-    "basic-memory": {
-      "command": "uvx",
-      "args": [
-        "basic-memory",
-        "mcp"
-      ]
-    }
-  }
-}
-```
-
-**Restart Claude Desktop**. You should see Basic Memory tools available in the "tools" menu in Claude Desktop (the little hammer icon in the bottom-right corner of the chat interface). Click it to view available tools.
-#### Fix Path to uv
-
-If you get an error that says `ENOENT` , this most likely means Claude Desktop could not find your `uv` installation. Make sure that you have `uv` installed per the instructions above, then:
-
-**Step 1: Find the absolute path to uvx**
+#### Step 1: Find the absolute path to uvx
 
 Open Terminal and run:
-
 ```bash
 which uvx
 ```
-
 This will show you the full path (e.g., `/Users/yourusername/.cargo/bin/uvx`).
 
-**Step 2: Edit Claude Desktop Configuration**
+#### Step 2: Edit Claude Desktop Configuration
 
-Edit the Claude Desktop config:
+Edit the configuration file located at `~/Library/Application Support/Claude/claude_desktop_config.json`:
 
 ```json
 {
@@ -85,15 +57,26 @@ Edit the Claude Desktop config:
 
 Replace `/absolute/path/to/uvx` with the actual path you found in Step 1.
 
-**Step 3: Restart Claude Desktop**
+> **Note**: Using absolute paths is necessary because Claude Desktop cannot access binaries in your user PATH.
+
+#### Step 3: Restart Claude Desktop
 
 Close and reopen Claude Desktop for the changes to take effect.
 
-### 3. Sync changes in real time
+### 3. Start the Sync Service
 
-> **Note**: The service will sync changes from your project directory in real time so they available for the AI assistant. 
+Start the sync service to monitor your files for changes:
+
+```bash
+# One-time sync
+basic-memory sync
+
+# For continuous monitoring (recommended)
+basic-memory sync --watch
+```
+
+The `--watch` flag enables automatic detection of file changes, keeping your knowledge base current.
 
-To disable realtime sync, you can update the config. See [[CLI Reference#sync]].
 ### 4. Staying Updated
 
 To update Basic Memory when new versions are released:
@@ -108,21 +91,6 @@ pip install --upgrade basic-memory
 
 > **Note**: After updating, you'll need to restart Claude Desktop and your sync process for changes to take effect.
 
-### 5. Change the default project directory
-
-By default, Basic Memory will create a project in the  `basic-memory` folder in your home directory. You can change this via the `project` [[CLI Reference#project|cli command]]. 
-
-```  
-# Add a new project  
-basic-memory project add work ~/work-basic-memory  
-  
-# Set the default project  
-basic-memory project default work  
-
-# List all configured projects  
-basic-memory project list  
-```
-
 ## Troubleshooting Installation
 
 ### Common Issues
@@ -134,35 +102,40 @@ If Claude cannot find Basic Memory tools:
 1. **Check absolute paths**: Ensure you're using complete absolute paths to uvx in the Claude Desktop configuration
 2. **Verify installation**: Run `basic-memory --version` in Terminal to confirm Basic Memory is installed
 3. **Restart applications**: Restart both Terminal and Claude Desktop after making configuration changes
-4. **Check sync status**: You can view the sync status by running `basic-memory status
-.
+4. **Check sync status**: Ensure `basic-memory sync --watch` is running
+
 #### Permission Issues
 
 If you encounter permission errors:
-
 1. Check that Basic Memory has access to create files in your home directory
 2. Ensure Claude Desktop has permission to execute the uvx command
 
 ## Creating Your First Knowledge Note
 
-1. **Open Claude Desktop** and start a new conversation.
+1. **Start the sync process** in a Terminal window:
+   ```bash
+   basic-memory sync --watch
+   ```
+   Keep this running in the background.
 
-2. **Have a natural conversation** about any topic:
+2. **Open Claude Desktop** and start a new conversation.
+
+3. **Have a natural conversation** about any topic:
    ```
    You: "Let's talk about coffee brewing methods I've been experimenting with."
    Claude: "I'd be happy to discuss coffee brewing methods..."
    You: "I've found that pour over gives more flavor clarity than French press..."
    ```
 
-3. **Ask Claude to create a note**:
+4. **Ask Claude to create a note**:
    ```
    You: "Could you create a note summarizing what we've discussed about coffee brewing?"
    ```
 
-4. **Confirm note creation**:
+5. **Confirm note creation**:
    Claude will confirm when the note has been created and where it's stored.
 
-5. **View the created file** in your `~/basic-memory` directory using any text editor or Obsidian.
+6. **View the created file** in your `~/basic-memory` directory using any text editor or Obsidian.
    The file structure will look similar to:
    ```markdown
    ---
@@ -180,12 +153,6 @@ If you encounter permission errors:
    - relates_to [[Other Coffee Topics]]
    ```
 
-5. **Start the sync process** in a Terminal window (optional):
-   ```bash
-   basic-memory sync --watch
-   ```
-   Keep this running in the background.
-
 ## Using Special Prompts
 
 Basic Memory includes special prompts that help you start conversations with context from your knowledge base:
@@ -271,15 +238,15 @@ basic-memory import claude conversations
 basic-memory import chatgpt
 ```
 
-After importing, the changes will be synced. Initial syncs may take a few moments. You can see info about your project by running `basic-memrory project info`.
+After importing, run `basic-memory sync` to index everything.
 
 ## Quick Tips
 
-- Basic Memory will sync changes from your project in real time.
+- Keep `basic-memory sync --watch` running in a terminal window
 - Use special prompts (Continue Conversation, Recent Activity, Search) to start contextual discussions
 - Build connections between notes for a richer knowledge graph
-- Use direct `memory://` URLs with a permalink when you need precise context. See [[User Guide#Using memory // URLs]]
-- Use git to version control your knowledge base (git integration is on the roadmap)
+- Use direct memory:// URLs when you need precise context
+- Use git to version control your knowledge base
 - Review and edit AI-generated notes for accuracy
 
 ## Next Steps

docs/Knowledge Format.md

@@ -144,19 +144,7 @@ permalink: auth-approaches-2024
 ---
 ```
 
-If not specified, one will be generated automatically from the title, if the note has has a frontmatter section. 
-
-By default a  notes' permalink value will not change if the file is moved. It's a **stable** identifier :). But if you'd rather permalinks are always updated when a file moves, you can set the config setting in the global config. 
-
-The config file for Basic Memory is in the home directory under `.basic-memory/config.json`.
-
-To change the behavior, set the following value:
-```
- ~/.basic-memory/config.json 
-{
-  "update_permalinks_on_move": true
-}
-```
+If not specified, one will be generated automatically from the title.
 
 ### Using memory:// URLs
 

docs/Technical Information.md

@@ -196,7 +196,7 @@ flowchart TD
     end
     
     BMCP <-->|"write_note() read_note()"| KnowledgeFiles
-    BMCP <-->|"search_notes() build_context()"| KnowledgeIndex
+    BMCP <-->|"search() build_context()"| KnowledgeIndex
     KnowledgeFiles <-.->|Sync Process| KnowledgeIndex
     KnowledgeFiles <-->|Direct Editing| Editors((Text Editors & Git))
     

docs/Welcome to Basic memory.md

@@ -24,13 +24,7 @@ Basic Memory connects you and AI assistants through shared knowledge:
 Both you and AI assistants like Claude can read from and write to the same knowledge base, creating a continuous
 learning environment where each conversation builds upon previous ones.
 
-## Pick up your conversation right where you left off
-
-- AI assistants can load context from local files in a new conversation
-- Notes are saved locally as Markdown files in real time
-- No project knowledge or special prompting required
-
-![[Claude-Obsidian-Demo.mp4]]
+![[Obsidian-CoffeeKnowledgeBase-examples-overlays.gif]]
 
 Basic Memory uses:
 

installer/installer.py

@@ -44,7 +44,7 @@ def update_claude_config():
 
     # Load existing config or create new
     if config_path.exists():
-        config = json.loads(config_path.read_text(encoding="utf-8"))
+        config = json.loads(config_path.read_text())
     else:
         config = {"mcpServers": {}}
 

llms-install.md

@@ -1,128 +0,0 @@
-# Basic Memory Installation Guide for LLMs
-
-This guide is specifically designed to help AI assistants like Cline install and configure Basic Memory. Follow these
-steps in order.
-
-## Installation Steps
-
-### 1. Install Basic Memory Package
-
-Use one of the following package managers to install:
-
-```bash
-# Install with uv (recommended)
-uv tool install basic-memory
-
-# Or with pip
-pip install basic-memory
-```
-
-### 2. Configure MCP Server
-
-Add the following to your config:
-
-```json
-{
-  "mcpServers": {
-    "basic-memory": {
-      "command": "uvx",
-      "args": [
-        "basic-memory",
-        "mcp"
-      ]
-    }
-  }
-}
-```
-
-For Claude Desktop, this file is located at:
-
-macOS: ~/Library/Application Support/Claude/claude_desktop_config.json
-Windows: %APPDATA%\Claude\claude_desktop_config.json
-
-### 3. Start Synchronization (optional)
-
-To synchronize files in real-time, run:
-
-```bash
-basic-memory sync --watch
-```
-
-Or for a one-time sync:
-
-```bash
-basic-memory sync
-```
-
-## Configuration Options
-
-### Custom Directory
-
-To use a directory other than the default `~/basic-memory`:
-
-```bash
-basic-memory project add custom-project /path/to/your/directory
-basic-memory project default custom-project
-```
-
-### Multiple Projects
-
-To manage multiple knowledge bases:
-
-```bash
-# List all projects
-basic-memory project list
-
-# Add a new project
-basic-memory project add work ~/work-basic-memory
-
-# Set default project
-basic-memory project default work
-```
-
-## Importing Existing Data
-
-### From Claude.ai
-
-```bash
-basic-memory import claude conversations path/to/conversations.json
-basic-memory import claude projects path/to/projects.json
-```
-
-### From ChatGPT
-
-```bash
-basic-memory import chatgpt path/to/conversations.json
-```
-
-### From MCP Memory Server
-
-```bash
-basic-memory import memory-json path/to/memory.json
-```
-
-## Troubleshooting
-
-If you encounter issues:
-
-1. Check that Basic Memory is properly installed:
-   ```bash
-   basic-memory --version
-   ```
-
-2. Verify the sync process is running:
-   ```bash
-   ps aux | grep basic-memory
-   ```
-
-3. Check sync output for errors:
-   ```bash
-   basic-memory sync --verbose
-   ```
-
-4. Check log output:
-   ```bash
-   cat ~/.basic-memory/basic-memory.log
-   ```
-
-For more detailed information, refer to the [full documentation](https://memory.basicmachines.co/).

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "basic-memory"
-version = "0.12.3"
+version = "0.9.0"
 description = "Local-first knowledge management combining Zettelkasten with knowledge graphs"
 readme = "README.md"
 requires-python = ">=3.12.1"
@@ -40,7 +40,6 @@ Documentation = "https://github.com/basicmachines-co/basic-memory#readme"
 
 [project.scripts]
 basic-memory = "basic_memory.cli.main:app"
-bm = "basic_memory.cli.main:app"
 
 [build-system]
 requires = ["hatchling"]

smithery.yaml

@@ -7,9 +7,11 @@ startCommand:
     type: object
     properties: {}
     description: No configuration required. This MCP server runs using the default command.
-  commandFunction: |-
+  commandFunction:
+    # A JS function that produces the CLI command based on the given config to start the MCP on stdio.
+    |-
     (config) => ({
       command: 'basic-memory',
       args: ['mcp']
     })
-  exampleConfig: {}
+  exampleConfig: {}

src/basic_memory/__init__.py

@@ -1,3 +1,3 @@
 """basic-memory - Local-first knowledge management combining Zettelkasten with knowledge graphs"""
 
-__version__ = "0.12.3"
+__version__ = "0.9.0"

src/basic_memory/api/app.py

@@ -7,24 +7,16 @@ from fastapi.exception_handlers import http_exception_handler
 from loguru import logger
 
 from basic_memory import db
-from basic_memory.api.routers import knowledge, memory, project_info, resource, search
-from basic_memory.config import config as project_config
-from basic_memory.services.initialization import initialize_app
+from basic_memory.config import config as app_config
+from basic_memory.api.routers import knowledge, search, memory, resource, project_info
 
 
 @asynccontextmanager
 async def lifespan(app: FastAPI):  # pragma: no cover
     """Lifecycle manager for the FastAPI app."""
-    # Initialize database and file sync services
-    watch_task = await initialize_app(project_config)
-
-    # proceed with startup
+    await db.run_migrations(app_config)
     yield
-
     logger.info("Shutting down Basic Memory API")
-    if watch_task:
-        watch_task.cancel()
-
     await db.shutdown_db()
 
 

src/basic_memory/api/routers/project_info_router.py

@@ -3,6 +3,9 @@
 import json
 from datetime import datetime
 
+from fastapi import APIRouter
+from sqlalchemy import text
+
 from basic_memory.config import config, config_manager
 from basic_memory.deps import (
     ProjectInfoRepositoryDep,
@@ -15,8 +18,6 @@ from basic_memory.schemas import (
     SystemStatus,
 )
 from basic_memory.sync.watch_service import WATCH_STATUS_JSON
-from fastapi import APIRouter
-from sqlalchemy import text
 
 router = APIRouter(prefix="/stats", tags=["statistics"])
 
@@ -261,7 +262,7 @@ async def get_system_status() -> SystemStatus:
     watch_status_path = config.home / ".basic-memory" / WATCH_STATUS_JSON
     if watch_status_path.exists():
         try:
-            watch_status = json.loads(watch_status_path.read_text(encoding="utf-8"))
+            watch_status = json.loads(watch_status_path.read_text())
         except Exception:  # pragma: no cover
             pass
 

src/basic_memory/cli/app.py

@@ -1,17 +1,18 @@
+import asyncio
 from typing import Optional
 
 import typer
 
+from basic_memory import db
+from basic_memory.config import config
+
 
 def version_callback(value: bool) -> None:
     """Show version and exit."""
     if value:  # pragma: no cover
         import basic_memory
-        from basic_memory.config import config
 
         typer.echo(f"Basic Memory version: {basic_memory.__version__}")
-        typer.echo(f"Current project: {config.project}")
-        typer.echo(f"Project path: {config.home}")
         raise typer.Exit()
 
 
@@ -20,12 +21,11 @@ app = typer.Typer(name="basic-memory")
 
 @app.callback()
 def app_callback(
-    ctx: typer.Context,
     project: Optional[str] = typer.Option(
         None,
         "--project",
         "-p",
-        help="Specify which project to use 1",
+        help="Specify which project to use",
         envvar="BASIC_MEMORY_PROJECT",
     ),
     version: Optional[bool] = typer.Option(
@@ -38,7 +38,6 @@ def app_callback(
     ),
 ) -> None:
     """Basic Memory - Local-first personal knowledge management."""
-
     # We use the project option to set the BASIC_MEMORY_PROJECT environment variable
     # The config module will pick this up when loading
     if project:  # pragma: no cover
@@ -58,13 +57,9 @@ def app_callback(
 
         config = new_config
 
-    # Run migrations for every command unless --version was specified
-    if not version and ctx.invoked_subcommand is not None:
-        from basic_memory.config import config
-        from basic_memory.services.initialization import ensure_initialize_database
-
-        ensure_initialize_database(config)
 
+# Run database migrations
+asyncio.run(db.run_migrations(config))
 
 # Register sub-command groups
 import_app = typer.Typer(help="Import data from various sources")

src/basic_memory/cli/commands/__init__.py

@@ -1,7 +1,7 @@
 """CLI commands for basic-memory."""
 
 from . import status, sync, db, import_memory_json, mcp, import_claude_conversations
-from . import import_claude_projects, import_chatgpt, tool, project
+from . import import_claude_projects, import_chatgpt, tool, project, project_info
 
 __all__ = [
     "status",
@@ -14,4 +14,5 @@ __all__ = [
     "import_chatgpt",
     "tool",
     "project",
+    "project_info",
 ]

src/basic_memory/cli/commands/db.py

@@ -1,13 +1,10 @@
 """Database management commands."""
 
-import asyncio
-
 import typer
 from loguru import logger
 
-from basic_memory import db
+from basic_memory.alembic import migrations
 from basic_memory.cli.app import app
-from basic_memory.config import config
 
 
 @app.command()
@@ -17,17 +14,7 @@ def reset(
     """Reset database (drop all tables and recreate)."""
     if typer.confirm("This will delete all data in your db. Are you sure?"):
         logger.info("Resetting database...")
-        # Get database path
-        db_path = config.database_path
-
-        # Delete the database file if it exists
-        if db_path.exists():
-            db_path.unlink()
-            logger.info(f"Database file deleted: {db_path}")
-
-        # Create a new empty database
-        asyncio.run(db.run_migrations(config))
-        logger.info("Database reset complete")
+        migrations.reset_database()
 
         if reindex:
             # Import and run sync

src/basic_memory/cli/commands/import_chatgpt.py

@@ -7,15 +7,16 @@ from pathlib import Path
 from typing import Dict, Any, List, Annotated, Set, Optional
 
 import typer
-from basic_memory.cli.app import import_app
-from basic_memory.config import config
-from basic_memory.markdown import EntityParser, MarkdownProcessor
-from basic_memory.markdown.schemas import EntityMarkdown, EntityFrontmatter
 from loguru import logger
 from rich.console import Console
 from rich.panel import Panel
 from rich.progress import Progress, SpinnerColumn, TextColumn, BarColumn
 
+from basic_memory.cli.app import import_app
+from basic_memory.config import config
+from basic_memory.markdown import EntityParser, MarkdownProcessor
+from basic_memory.markdown.schemas import EntityMarkdown, EntityFrontmatter
+
 console = Console()
 
 
@@ -166,7 +167,7 @@ async def process_chatgpt_json(
         read_task = progress.add_task("Reading chat data...", total=None)
 
         # Read conversations
-        conversations = json.loads(json_path.read_text(encoding="utf-8"))
+        conversations = json.loads(json_path.read_text())
         progress.update(read_task, total=len(conversations))
 
         # Process each conversation

src/basic_memory/cli/commands/import_claude_conversations.py

@@ -7,15 +7,16 @@ from pathlib import Path
 from typing import Dict, Any, List, Annotated
 
 import typer
-from basic_memory.cli.app import claude_app
-from basic_memory.config import config
-from basic_memory.markdown import EntityParser, MarkdownProcessor
-from basic_memory.markdown.schemas import EntityMarkdown, EntityFrontmatter
 from loguru import logger
 from rich.console import Console
 from rich.panel import Panel
 from rich.progress import Progress, SpinnerColumn, TextColumn, BarColumn
 
+from basic_memory.cli.app import claude_app
+from basic_memory.config import config
+from basic_memory.markdown import EntityParser, MarkdownProcessor
+from basic_memory.markdown.schemas import EntityMarkdown, EntityFrontmatter
+
 console = Console()
 
 
@@ -123,7 +124,7 @@ async def process_conversations_json(
         read_task = progress.add_task("Reading chat data...", total=None)
 
         # Read chat data - handle array of arrays format
-        data = json.loads(json_path.read_text(encoding="utf-8"))
+        data = json.loads(json_path.read_text())
         conversations = [chat for chat in data]
         progress.update(read_task, total=len(conversations))
 

src/basic_memory/cli/commands/import_claude_projects.py

@@ -6,15 +6,16 @@ from pathlib import Path
 from typing import Dict, Any, Annotated, Optional
 
 import typer
-from basic_memory.cli.app import claude_app
-from basic_memory.config import config
-from basic_memory.markdown import EntityParser, MarkdownProcessor
-from basic_memory.markdown.schemas import EntityMarkdown, EntityFrontmatter
 from loguru import logger
 from rich.console import Console
 from rich.panel import Panel
 from rich.progress import Progress, SpinnerColumn, TextColumn, BarColumn
 
+from basic_memory.cli.app import claude_app
+from basic_memory.config import config
+from basic_memory.markdown import EntityParser, MarkdownProcessor
+from basic_memory.markdown.schemas import EntityMarkdown, EntityFrontmatter
+
 console = Console()
 
 
@@ -102,7 +103,7 @@ async def process_projects_json(
         read_task = progress.add_task("Reading project data...", total=None)
 
         # Read project data
-        data = json.loads(json_path.read_text(encoding="utf-8"))
+        data = json.loads(json_path.read_text())
         progress.update(read_task, total=len(data))
 
         # Track import counts

src/basic_memory/cli/commands/import_memory_json.py

@@ -38,7 +38,7 @@ async def process_memory_json(
         read_task = progress.add_task("Reading memory.json...", total=None)
 
         # First pass - collect entities and relations
-        with open(json_path, encoding="utf-8") as f:
+        with open(json_path) as f:
             lines = f.readlines()
             progress.update(read_task, total=len(lines))
 

src/basic_memory/cli/commands/mcp.py

@@ -1,7 +1,10 @@
 """MCP server command."""
 
+from loguru import logger
+
 import basic_memory
 from basic_memory.cli.app import app
+from basic_memory.config import config
 
 # Import mcp instance
 from basic_memory.mcp.server import mcp as mcp_server  # pragma: no cover
@@ -12,24 +15,12 @@ import basic_memory.mcp.tools  # noqa: F401  # pragma: no cover
 
 @app.command()
 def mcp():  # pragma: no cover
-    """Run the MCP server"""
-    from basic_memory.config import config
-    import asyncio
-    from basic_memory.services.initialization import initialize_database
+    """Run the MCP server for Claude Desktop integration."""
+    home_dir = config.home
+    project_name = config.project
 
-    # First, run just the database migrations synchronously
-    asyncio.run(initialize_database(config))
+    logger.info(f"Starting Basic Memory MCP server {basic_memory.__version__}")
+    logger.info(f"Project: {project_name}")
+    logger.info(f"Project directory: {home_dir}")
 
-    # Load config to check if sync is enabled
-    from basic_memory.config import config_manager
-
-    basic_memory_config = config_manager.load_config()
-
-    if basic_memory_config.sync_changes:
-        # For now, we'll just log that sync will be handled by the MCP server
-        from loguru import logger
-
-        logger.info("File sync will be handled by the MCP server")
-
-    # Start the MCP server
     mcp_server.run()

src/basic_memory/cli/commands/project.py

@@ -1,6 +1,5 @@
 """Command module for basic-memory project management."""
 
-import asyncio
 import os
 from pathlib import Path
 
@@ -10,12 +9,6 @@ from rich.table import Table
 
 from basic_memory.cli.app import app
 from basic_memory.config import ConfigManager, config
-from basic_memory.mcp.tools.project_info import project_info
-import json
-from datetime import datetime
-
-from rich.panel import Panel
-from rich.tree import Tree
 
 console = Console()
 
@@ -99,22 +92,12 @@ def remove_project(
 def set_default_project(
     name: str = typer.Argument(..., help="Name of the project to set as default"),
 ) -> None:
-    """Set the default project and activate it for the current session."""
+    """Set the default project."""
     config_manager = ConfigManager()
 
     try:
-        # Set the default project
         config_manager.set_default_project(name)
-
-        # Also activate it for the current session by setting the environment variable
-        os.environ["BASIC_MEMORY_PROJECT"] = name
-
-        # Reload configuration to apply the change
-        from importlib import reload
-        from basic_memory import config as config_module
-
-        reload(config_module)
-        console.print(f"[green]Project '{name}' set as default and activated[/green]")
+        console.print(f"[green]Project '{name}' set as default[/green]")
     except ValueError as e:  # pragma: no cover
         console.print(f"[red]Error: {e}[/red]")
         raise typer.Exit(1)
@@ -134,152 +117,3 @@ def show_current_project() -> None:
     except ValueError:  # pragma: no cover
         console.print(f"[yellow]Warning: Project '{current}' not found in configuration[/yellow]")
         console.print(f"Using default project: [cyan]{config_manager.default_project}[/cyan]")
-
-
-@project_app.command("info")
-def display_project_info(
-    json_output: bool = typer.Option(False, "--json", help="Output in JSON format"),
-):
-    """Display detailed information and statistics about the current project."""
-    try:
-        # Get project info
-        info = asyncio.run(project_info())
-
-        if json_output:
-            # Convert to JSON and print
-            print(json.dumps(info.model_dump(), indent=2, default=str))
-        else:
-            # Create rich display
-            console = Console()
-
-            # Project configuration section
-            console.print(
-                Panel(
-                    f"[bold]Project:[/bold] {info.project_name}\n"
-                    f"[bold]Path:[/bold] {info.project_path}\n"
-                    f"[bold]Default Project:[/bold] {info.default_project}\n",
-                    title="📊 Basic Memory Project Info",
-                    expand=False,
-                )
-            )
-
-            # Statistics section
-            stats_table = Table(title="📈 Statistics")
-            stats_table.add_column("Metric", style="cyan")
-            stats_table.add_column("Count", style="green")
-
-            stats_table.add_row("Entities", str(info.statistics.total_entities))
-            stats_table.add_row("Observations", str(info.statistics.total_observations))
-            stats_table.add_row("Relations", str(info.statistics.total_relations))
-            stats_table.add_row(
-                "Unresolved Relations", str(info.statistics.total_unresolved_relations)
-            )
-            stats_table.add_row("Isolated Entities", str(info.statistics.isolated_entities))
-
-            console.print(stats_table)
-
-            # Entity types
-            if info.statistics.entity_types:
-                entity_types_table = Table(title="📑 Entity Types")
-                entity_types_table.add_column("Type", style="blue")
-                entity_types_table.add_column("Count", style="green")
-
-                for entity_type, count in info.statistics.entity_types.items():
-                    entity_types_table.add_row(entity_type, str(count))
-
-                console.print(entity_types_table)
-
-            # Most connected entities
-            if info.statistics.most_connected_entities:
-                connected_table = Table(title="🔗 Most Connected Entities")
-                connected_table.add_column("Title", style="blue")
-                connected_table.add_column("Permalink", style="cyan")
-                connected_table.add_column("Relations", style="green")
-
-                for entity in info.statistics.most_connected_entities:
-                    connected_table.add_row(
-                        entity["title"], entity["permalink"], str(entity["relation_count"])
-                    )
-
-                console.print(connected_table)
-
-            # Recent activity
-            if info.activity.recently_updated:
-                recent_table = Table(title="🕒 Recent Activity")
-                recent_table.add_column("Title", style="blue")
-                recent_table.add_column("Type", style="cyan")
-                recent_table.add_column("Last Updated", style="green")
-
-                for entity in info.activity.recently_updated[:5]:  # Show top 5
-                    updated_at = (
-                        datetime.fromisoformat(entity["updated_at"])
-                        if isinstance(entity["updated_at"], str)
-                        else entity["updated_at"]
-                    )
-                    recent_table.add_row(
-                        entity["title"],
-                        entity["entity_type"],
-                        updated_at.strftime("%Y-%m-%d %H:%M"),
-                    )
-
-                console.print(recent_table)
-
-            # System status
-            system_tree = Tree("🖥️ System Status")
-            system_tree.add(f"Basic Memory version: [bold green]{info.system.version}[/bold green]")
-            system_tree.add(
-                f"Database: [cyan]{info.system.database_path}[/cyan] ([green]{info.system.database_size}[/green])"
-            )
-
-            # Watch status
-            if info.system.watch_status:  # pragma: no cover
-                watch_branch = system_tree.add("Watch Service")
-                running = info.system.watch_status.get("running", False)
-                status_color = "green" if running else "red"
-                watch_branch.add(
-                    f"Status: [bold {status_color}]{'Running' if running else 'Stopped'}[/bold {status_color}]"
-                )
-
-                if running:
-                    start_time = (
-                        datetime.fromisoformat(info.system.watch_status.get("start_time", ""))
-                        if isinstance(info.system.watch_status.get("start_time"), str)
-                        else info.system.watch_status.get("start_time")
-                    )
-                    watch_branch.add(
-                        f"Running since: [cyan]{start_time.strftime('%Y-%m-%d %H:%M')}[/cyan]"
-                    )
-                    watch_branch.add(
-                        f"Files synced: [green]{info.system.watch_status.get('synced_files', 0)}[/green]"
-                    )
-                    watch_branch.add(
-                        f"Errors: [{'red' if info.system.watch_status.get('error_count', 0) > 0 else 'green'}]{info.system.watch_status.get('error_count', 0)}[/{'red' if info.system.watch_status.get('error_count', 0) > 0 else 'green'}]"
-                    )
-            else:
-                system_tree.add("[yellow]Watch service not running[/yellow]")
-
-            console.print(system_tree)
-
-            # Available projects
-            projects_table = Table(title="📁 Available Projects")
-            projects_table.add_column("Name", style="blue")
-            projects_table.add_column("Path", style="cyan")
-            projects_table.add_column("Default", style="green")
-
-            for name, path in info.available_projects.items():
-                is_default = name == info.default_project
-                projects_table.add_row(name, path, "✓" if is_default else "")
-
-            console.print(projects_table)
-
-            # Timestamp
-            current_time = (
-                datetime.fromisoformat(str(info.system.timestamp))
-                if isinstance(info.system.timestamp, str)
-                else info.system.timestamp
-            )
-            console.print(f"\nTimestamp: [cyan]{current_time.strftime('%Y-%m-%d %H:%M:%S')}[/cyan]")
-
-    except Exception as e:  # pragma: no cover
-        typer.echo(f"Error getting project info: {e}", err=True)
-        raise typer.Exit(1)

src/basic_memory/cli/commands/project_info.py

@@ -0,0 +1,167 @@
+"""CLI command for project info status."""
+
+import asyncio
+import json
+from datetime import datetime
+
+import typer
+from rich.console import Console
+from rich.table import Table
+from rich.panel import Panel
+from rich.tree import Tree
+
+from basic_memory.cli.app import app
+from basic_memory.mcp.tools.project_info import project_info
+
+
+info_app = typer.Typer()
+app.add_typer(info_app, name="info", help="Get information about your Basic Memory project")
+
+
+@info_app.command("stats")
+def display_project_info(
+    json_output: bool = typer.Option(False, "--json", help="Output in JSON format"),
+):
+    """Display detailed information and statistics about the current project."""
+    try:
+        # Get project info
+        info = asyncio.run(project_info())
+
+        if json_output:
+            # Convert to JSON and print
+            print(json.dumps(info.model_dump(), indent=2, default=str))
+        else:
+            # Create rich display
+            console = Console()
+
+            # Project configuration section
+            console.print(
+                Panel(
+                    f"[bold]Project:[/bold] {info.project_name}\n"
+                    f"[bold]Path:[/bold] {info.project_path}\n"
+                    f"[bold]Default Project:[/bold] {info.default_project}\n",
+                    title="📊 Basic Memory Project Info",
+                    expand=False,
+                )
+            )
+
+            # Statistics section
+            stats_table = Table(title="📈 Statistics")
+            stats_table.add_column("Metric", style="cyan")
+            stats_table.add_column("Count", style="green")
+
+            stats_table.add_row("Entities", str(info.statistics.total_entities))
+            stats_table.add_row("Observations", str(info.statistics.total_observations))
+            stats_table.add_row("Relations", str(info.statistics.total_relations))
+            stats_table.add_row(
+                "Unresolved Relations", str(info.statistics.total_unresolved_relations)
+            )
+            stats_table.add_row("Isolated Entities", str(info.statistics.isolated_entities))
+
+            console.print(stats_table)
+
+            # Entity types
+            if info.statistics.entity_types:
+                entity_types_table = Table(title="📑 Entity Types")
+                entity_types_table.add_column("Type", style="blue")
+                entity_types_table.add_column("Count", style="green")
+
+                for entity_type, count in info.statistics.entity_types.items():
+                    entity_types_table.add_row(entity_type, str(count))
+
+                console.print(entity_types_table)
+
+            # Most connected entities
+            if info.statistics.most_connected_entities:
+                connected_table = Table(title="🔗 Most Connected Entities")
+                connected_table.add_column("Title", style="blue")
+                connected_table.add_column("Permalink", style="cyan")
+                connected_table.add_column("Relations", style="green")
+
+                for entity in info.statistics.most_connected_entities:
+                    connected_table.add_row(
+                        entity["title"], entity["permalink"], str(entity["relation_count"])
+                    )
+
+                console.print(connected_table)
+
+            # Recent activity
+            if info.activity.recently_updated:
+                recent_table = Table(title="🕒 Recent Activity")
+                recent_table.add_column("Title", style="blue")
+                recent_table.add_column("Type", style="cyan")
+                recent_table.add_column("Last Updated", style="green")
+
+                for entity in info.activity.recently_updated[:5]:  # Show top 5
+                    updated_at = (
+                        datetime.fromisoformat(entity["updated_at"])
+                        if isinstance(entity["updated_at"], str)
+                        else entity["updated_at"]
+                    )
+                    recent_table.add_row(
+                        entity["title"],
+                        entity["entity_type"],
+                        updated_at.strftime("%Y-%m-%d %H:%M"),
+                    )
+
+                console.print(recent_table)
+
+            # System status
+            system_tree = Tree("🖥️ System Status")
+            system_tree.add(f"Basic Memory version: [bold green]{info.system.version}[/bold green]")
+            system_tree.add(
+                f"Database: [cyan]{info.system.database_path}[/cyan] ([green]{info.system.database_size}[/green])"
+            )
+
+            # Watch status
+            if info.system.watch_status:  # pragma: no cover
+                watch_branch = system_tree.add("Watch Service")
+                running = info.system.watch_status.get("running", False)
+                status_color = "green" if running else "red"
+                watch_branch.add(
+                    f"Status: [bold {status_color}]{'Running' if running else 'Stopped'}[/bold {status_color}]"
+                )
+
+                if running:
+                    start_time = (
+                        datetime.fromisoformat(info.system.watch_status.get("start_time", ""))
+                        if isinstance(info.system.watch_status.get("start_time"), str)
+                        else info.system.watch_status.get("start_time")
+                    )
+                    watch_branch.add(
+                        f"Running since: [cyan]{start_time.strftime('%Y-%m-%d %H:%M')}[/cyan]"
+                    )
+                    watch_branch.add(
+                        f"Files synced: [green]{info.system.watch_status.get('synced_files', 0)}[/green]"
+                    )
+                    watch_branch.add(
+                        f"Errors: [{'red' if info.system.watch_status.get('error_count', 0) > 0 else 'green'}]{info.system.watch_status.get('error_count', 0)}[/{'red' if info.system.watch_status.get('error_count', 0) > 0 else 'green'}]"
+                    )
+            else:
+                system_tree.add("[yellow]Watch service not running[/yellow]")
+
+            console.print(system_tree)
+
+            # Available projects
+            projects_table = Table(title="📁 Available Projects")
+            projects_table.add_column("Name", style="blue")
+            projects_table.add_column("Path", style="cyan")
+            projects_table.add_column("Default", style="green")
+
+            for name, path in info.available_projects.items():
+                is_default = name == info.default_project
+                projects_table.add_row(name, path, "✓" if is_default else "")
+
+            console.print(projects_table)
+
+            # Timestamp
+            current_time = (
+                datetime.fromisoformat(str(info.system.timestamp))
+                if isinstance(info.system.timestamp, str)
+                else info.system.timestamp
+            )
+            console.print(f"\nTimestamp: [cyan]{current_time.strftime('%Y-%m-%d %H:%M:%S')}[/cyan]")
+
+    except Exception as e:  # pragma: no cover
+        typer.echo(f"Error getting project info: {e}", err=True)
+        raise typer.Exit(1)

src/basic_memory/cli/commands/sync.py

@@ -70,7 +70,6 @@ async def get_sync_service():  # pragma: no cover
 
     # Create sync service
     sync_service = SyncService(
-        config=config,
         entity_service=entity_service,
         entity_parser=entity_parser,
         entity_repository=entity_repository,
@@ -179,14 +178,14 @@ async def run_sync(verbose: bool = False, watch: bool = False, console_status: b
         )
 
         # full sync - no progress bars in watch mode
-        await sync_service.sync(config.home)
+        await sync_service.sync(config.home, show_progress=False)
 
         # watch changes
         await watch_service.run()  # pragma: no cover
     else:
-        # one time sync
+        # one time sync - use progress bars for better UX
         logger.info("Running one-time sync")
-        knowledge_changes = await sync_service.sync(config.home)
+        knowledge_changes = await sync_service.sync(config.home, show_progress=True)
 
         # Log results
         duration_ms = int((time.time() - start_time) * 1000)
@@ -237,11 +236,11 @@ def sync(
         if not isinstance(e, typer.Exit):
             logger.exception(
                 "Sync command failed",
-                f"project={config.project},"
-                f"error={str(e)},"
-                f"error_type={type(e).__name__},"
-                f"watch_mode={watch},"
-                f"directory={str(config.home)}",
+                project=config.project,
+                error=str(e),
+                error_type=type(e).__name__,
+                watch_mode=watch,
+                directory=str(config.home),
             )
             typer.echo(f"Error during sync: {e}", err=True)
             raise typer.Exit(1)

src/basic_memory/cli/commands/tool.py

@@ -2,32 +2,34 @@
 
 import asyncio
 import sys
-from typing import Annotated, List, Optional
+from typing import Optional, List, Annotated
 
 import typer
 from loguru import logger
 from rich import print as rprint
 
 from basic_memory.cli.app import app
+from basic_memory.mcp.tools import build_context as mcp_build_context
+from basic_memory.mcp.tools import read_note as mcp_read_note
+from basic_memory.mcp.tools import recent_activity as mcp_recent_activity
+from basic_memory.mcp.tools import search as mcp_search
+from basic_memory.mcp.tools import write_note as mcp_write_note
 
 # Import prompts
 from basic_memory.mcp.prompts.continue_conversation import (
     continue_conversation as mcp_continue_conversation,
 )
+
 from basic_memory.mcp.prompts.recent_activity import (
     recent_activity_prompt as recent_activity_prompt,
 )
-from basic_memory.mcp.tools import build_context as mcp_build_context
-from basic_memory.mcp.tools import read_note as mcp_read_note
-from basic_memory.mcp.tools import recent_activity as mcp_recent_activity
-from basic_memory.mcp.tools import search_notes as mcp_search
-from basic_memory.mcp.tools import write_note as mcp_write_note
+
 from basic_memory.schemas.base import TimeFrame
 from basic_memory.schemas.memory import MemoryUrl
-from basic_memory.schemas.search import SearchItemType
+from basic_memory.schemas.search import SearchQuery, SearchItemType
 
 tool_app = typer.Typer()
-app.add_typer(tool_app, name="tool", help="Access to MCP tools via CLI")
+app.add_typer(tool_app, name="tool", help="Direct access to MCP tools via CLI")
 
 
 @tool_app.command()
@@ -101,7 +103,6 @@ def write_note(
 
 @tool_app.command()
 def read_note(identifier: str, page: int = 1, page_size: int = 10):
-    """Read a markdown note from the knowledge base."""
     try:
         note = asyncio.run(mcp_read_note(identifier, page, page_size))
         rprint(note)
@@ -121,7 +122,6 @@ def build_context(
     page_size: int = 10,
     max_related: int = 10,
 ):
-    """Get context needed to continue a discussion."""
     try:
         context = asyncio.run(
             mcp_build_context(
@@ -154,7 +154,6 @@ def recent_activity(
     page_size: int = 10,
     max_related: int = 10,
 ):
-    """Get recent activity across the knowledge base."""
     try:
         context = asyncio.run(
             mcp_recent_activity(
@@ -178,8 +177,8 @@ def recent_activity(
         raise
 
 
-@tool_app.command("search-notes")
-def search_notes(
+@tool_app.command()
+def search(
     query: str,
     permalink: Annotated[bool, typer.Option("--permalink", help="Search permalink values")] = False,
     title: Annotated[bool, typer.Option("--title", help="Search title values")] = False,
@@ -190,34 +189,18 @@ def search_notes(
     page: int = 1,
     page_size: int = 10,
 ):
-    """Search across all content in the knowledge base."""
     if permalink and title:  # pragma: no cover
         print("Cannot search both permalink and title")
         raise typer.Abort()
 
     try:
-        if permalink and title:  # pragma: no cover
-            typer.echo(
-                "Use either --permalink or --title, not both. Exiting.",
-                err=True,
-            )
-            raise typer.Exit(1)
-
-        # set search type
-        search_type = ("permalink" if permalink else None,)
-        search_type = ("permalink_match" if permalink and "*" in query else None,)
-        search_type = ("title" if title else None,)
-        search_type = "text" if search_type is None else search_type
-
-        results = asyncio.run(
-            mcp_search(
-                query,
-                search_type=search_type,
-                page=page,
-                after_date=after_date,
-                page_size=page_size,
-            )
+        search_query = SearchQuery(
+            permalink_match=query if permalink else None,
+            text=query if not (permalink or title) else None,
+            title=query if title else None,
+            after_date=after_date,
         )
+        results = asyncio.run(mcp_search(query=search_query, page=page, page_size=page_size))
         # Use json module for more controlled serialization
         import json
 

src/basic_memory/cli/main.py

@@ -1,26 +1,58 @@
 """Main CLI entry point for basic-memory."""  # pragma: no cover
 
 from basic_memory.cli.app import app  # pragma: no cover
+import typer
 
 # Register commands
 from basic_memory.cli.commands import (  # noqa: F401  # pragma: no cover
-    db,
-    import_chatgpt,
-    import_claude_conversations,
-    import_claude_projects,
-    import_memory_json,
-    mcp,
-    project,
     status,
     sync,
+    db,
+    import_memory_json,
+    mcp,
+    import_claude_conversations,
+    import_claude_projects,
+    import_chatgpt,
     tool,
+    project,
 )
-from basic_memory.config import config
-from basic_memory.services.initialization import ensure_initialization
+
+
+# Version command
+@app.callback(invoke_without_command=True)
+def main(
+    ctx: typer.Context,
+    project: str = typer.Option(  # noqa
+        "main",
+        "--project",
+        "-p",
+        help="Specify which project to use",
+        envvar="BASIC_MEMORY_PROJECT",
+    ),
+    version: bool = typer.Option(
+        False,
+        "--version",
+        "-V",
+        help="Show version information and exit.",
+        is_eager=True,
+    ),
+):
+    """Basic Memory - Local-first personal knowledge management system."""
+    if version:  # pragma: no cover
+        from basic_memory import __version__
+        from basic_memory.config import config
+
+        typer.echo(f"Basic Memory v{__version__}")
+        typer.echo(f"Current project: {config.project}")
+        typer.echo(f"Project path: {config.home}")
+        raise typer.Exit()
+
+    # Handle project selection via environment variable
+    if project:
+        import os
+
+        os.environ["BASIC_MEMORY_PROJECT"] = project
+
 
 if __name__ == "__main__":  # pragma: no cover
-    # Run initialization if we are starting as a module
-    ensure_initialization(config)
-
-    # start the app
     app()

src/basic_memory/config.py

@@ -35,14 +35,10 @@ class ProjectConfig(BaseSettings):
 
     # Watch service configuration
     sync_delay: int = Field(
-        default=1000, description="Milliseconds to wait after changes before syncing", gt=0
+        default=500, description="Milliseconds to wait after changes before syncing", gt=0
     )
 
-    # update permalinks on move
-    update_permalinks_on_move: bool = Field(
-        default=False,
-        description="Whether to update permalinks when files are moved or renamed. default (False)",
-    )
+    log_level: str = "DEBUG"
 
     model_config = SettingsConfigDict(
         env_prefix="BASIC_MEMORY_",
@@ -81,18 +77,6 @@ class BasicMemoryConfig(BaseSettings):
         description="Name of the default project to use",
     )
 
-    log_level: str = "INFO"
-
-    update_permalinks_on_move: bool = Field(
-        default=False,
-        description="Whether to update permalinks when files are moved or renamed. default (False)",
-    )
-
-    sync_changes: bool = Field(
-        default=True,
-        description="Whether to sync changes in real time. default (True)",
-    )
-
     model_config = SettingsConfigDict(
         env_prefix="BASIC_MEMORY_",
         extra="ignore",
@@ -127,7 +111,7 @@ class ConfigManager:
         """Load configuration from file or create default."""
         if self.config_file.exists():
             try:
-                data = json.loads(self.config_file.read_text(encoding="utf-8"))
+                data = json.loads(self.config_file.read_text())
                 return BasicMemoryConfig(**data)
             except Exception as e:
                 logger.error(f"Failed to load config: {e}")
@@ -210,14 +194,9 @@ def get_project_config(project_name: Optional[str] = None) -> ProjectConfig:
         "BASIC_MEMORY_PROJECT", project_name or config_manager.default_project
     )
 
-    update_permalinks_on_move = config_manager.load_config().update_permalinks_on_move
     try:
         project_path = config_manager.get_project_path(actual_project_name)
-        return ProjectConfig(
-            home=project_path,
-            project=actual_project_name,
-            update_permalinks_on_move=update_permalinks_on_move,
-        )
+        return ProjectConfig(home=project_path, project=actual_project_name)
     except ValueError:  # pragma: no cover
         logger.warning(f"Project '{actual_project_name}' not found, using default")
         project_path = config_manager.get_project_path(config_manager.default_project)
@@ -235,48 +214,11 @@ user_home = Path.home()
 log_dir = user_home / DATA_DIR_NAME
 log_dir.mkdir(parents=True, exist_ok=True)
 
-
-def get_process_name():  # pragma: no cover
-    """
-    get the type of process for logging
-    """
-    import sys
-
-    if "sync" in sys.argv:
-        return "sync"
-    elif "mcp" in sys.argv:
-        return "mcp"
-    elif "cli" in sys.argv:
-        return "cli"
-    else:
-        return "api"
-
-
-process_name = get_process_name()
-
-# Global flag to track if logging has been set up
-_LOGGING_SETUP = False
-
-
-def setup_basic_memory_logging():  # pragma: no cover
-    """Set up logging for basic-memory, ensuring it only happens once."""
-    global _LOGGING_SETUP
-    if _LOGGING_SETUP:
-        # We can't log before logging is set up
-        # print("Skipping duplicate logging setup")
-        return
-
-    setup_logging(
-        env=config.env,
-        home_dir=user_home,  # Use user home for logs
-        log_level=config_manager.load_config().log_level,
-        log_file=f"{DATA_DIR_NAME}/basic-memory-{process_name}.log",
-        console=False,
-    )
-
-    logger.info(f"Basic Memory {basic_memory.__version__} (Project: {config.project})")
-    _LOGGING_SETUP = True
-
-
-# Set up logging
-setup_basic_memory_logging()
+setup_logging(
+    env=config.env,
+    home_dir=user_home,  # Use user home for logs
+    log_level=config.log_level,
+    log_file=f"{DATA_DIR_NAME}/basic-memory.log",
+    console=False,
+)
+logger.info(f"Starting Basic Memory {basic_memory.__version__} (Project: {config.project})")

src/basic_memory/db.py

@@ -146,9 +146,7 @@ async def engine_session_factory(
             _session_maker = None
 
 
-async def run_migrations(
-    app_config: ProjectConfig, database_type=DatabaseType.FILESYSTEM
-):  # pragma: no cover
+async def run_migrations(app_config: ProjectConfig, database_type=DatabaseType.FILESYSTEM):
     """Run any pending alembic migrations."""
     logger.info("Running database migrations...")
     try:

src/basic_memory/file_utils.py

@@ -85,7 +85,7 @@ async def write_file_atomic(path: FilePath, content: str) -> None:
     temp_path = path_obj.with_suffix(".tmp")
 
     try:
-        temp_path.write_text(content, encoding="utf-8")
+        temp_path.write_text(content)
         temp_path.replace(path_obj)
         logger.debug("Wrote file atomically", path=str(path_obj), content_length=len(content))
     except Exception as e:  # pragma: no cover
@@ -104,9 +104,6 @@ def has_frontmatter(content: str) -> bool:
     Returns:
         True if content has valid frontmatter markers (---), False otherwise
     """
-    if not content:
-        return False
-
     content = content.strip()
     if not content.startswith("---"):
         return False
@@ -206,7 +203,7 @@ async def update_frontmatter(path: FilePath, updates: Dict[str, Any]) -> str:
         path_obj = Path(path) if isinstance(path, str) else path
 
         # Read current content
-        content = path_obj.read_text(encoding="utf-8")
+        content = path_obj.read_text()
 
         # Parse current frontmatter
         current_fm = {}
@@ -218,7 +215,7 @@ async def update_frontmatter(path: FilePath, updates: Dict[str, Any]) -> str:
         new_fm = {**current_fm, **updates}
 
         # Write new file with updated frontmatter
-        yaml_fm = yaml.dump(new_fm, sort_keys=False, allow_unicode=True)
+        yaml_fm = yaml.dump(new_fm, sort_keys=False)
         final_content = f"---\n{yaml_fm}---\n\n{content.strip()}"
 
         logger.debug("Updating frontmatter", path=str(path_obj), update_keys=list(updates.keys()))

src/basic_memory/markdown/entity_parser.py

@@ -4,22 +4,21 @@ Uses markdown-it with plugins to parse structured data from markdown content.
 """
 
 from dataclasses import dataclass, field
-from datetime import datetime
 from pathlib import Path
+from datetime import datetime
 from typing import Any, Optional
-
 import dateparser
-import frontmatter
+
 from markdown_it import MarkdownIt
+import frontmatter
 
 from basic_memory.markdown.plugins import observation_plugin, relation_plugin
 from basic_memory.markdown.schemas import (
-    EntityFrontmatter,
     EntityMarkdown,
+    EntityFrontmatter,
     Observation,
     Relation,
 )
-from basic_memory.utils import parse_tags
 
 md = MarkdownIt().use(observation_plugin).use(relation_plugin)
 
@@ -57,11 +56,11 @@ def parse(content: str) -> EntityContent:
     )
 
 
-# def parse_tags(tags: Any) -> list[str]:
-#     """Parse tags into list of strings."""
-#     if isinstance(tags, (list, tuple)):
-#         return [str(t).strip() for t in tags if str(t).strip()]
-#     return [t.strip() for t in tags.split(",") if t.strip()]
+def parse_tags(tags: Any) -> list[str]:
+    """Parse tags into list of strings."""
+    if isinstance(tags, (list, tuple)):
+        return [str(t).strip() for t in tags if str(t).strip()]
+    return [t.strip() for t in tags.split(",") if t.strip()]
 
 
 class EntityParser:
@@ -92,36 +91,25 @@ class EntityParser:
     async def parse_file(self, path: Path | str) -> EntityMarkdown:
         """Parse markdown file into EntityMarkdown."""
 
-        # TODO move to api endpoint to check if absolute path was requested
-        # Check if the path is already absolute
-        if (
-            isinstance(path, Path)
-            and path.is_absolute()
-            or (isinstance(path, str) and Path(path).is_absolute())
-        ):
-            absolute_path = Path(path)
-        else:
-            absolute_path = self.base_path / path
-
+        absolute_path = self.base_path / path
         # Parse frontmatter and content using python-frontmatter
-        file_content = absolute_path.read_text(encoding="utf-8")
-        return await self.parse_file_content(absolute_path, file_content)
+        post = frontmatter.load(str(absolute_path))
 
-    async def parse_file_content(self, absolute_path, file_content):
-        post = frontmatter.loads(file_content)
         # Extract file stat info
         file_stats = absolute_path.stat()
+
         metadata = post.metadata
-        metadata["title"] = post.metadata.get("title", absolute_path.stem)
+        metadata["title"] = post.metadata.get("title", absolute_path.name)
         metadata["type"] = post.metadata.get("type", "note")
-        tags = parse_tags(post.metadata.get("tags", []))  # pyright: ignore
-        if tags:
-            metadata["tags"] = tags
+        metadata["tags"] = parse_tags(post.metadata.get("tags", []))
+
         # frontmatter
         entity_frontmatter = EntityFrontmatter(
             metadata=post.metadata,
         )
+
         entity_content = parse(post.content)
+
         return EntityMarkdown(
             frontmatter=entity_frontmatter,
             content=post.content,

src/basic_memory/markdown/markdown_processor.py

@@ -83,7 +83,7 @@ class MarkdownProcessor:
         """
         # Dirty check if needed
         if expected_checksum is not None:
-            current_content = path.read_text(encoding="utf-8")
+            current_content = path.read_text()
             current_checksum = await file_utils.compute_checksum(current_content)
             if current_checksum != expected_checksum:
                 raise DirtyFileError(f"File {path} has been modified")

src/basic_memory/markdown/schemas.py

@@ -42,7 +42,7 @@ class EntityFrontmatter(BaseModel):
 
     @property
     def tags(self) -> List[str]:
-        return self.metadata.get("tags") if self.metadata else None  # pyright: ignore
+        return self.metadata.get("tags") if self.metadata else []  # pyright: ignore
 
     @property
     def title(self) -> str:

src/basic_memory/markdown/utils.py

@@ -1,14 +1,14 @@
 """Utilities for converting between markdown and entity models."""
 
 from pathlib import Path
-from typing import Any, Optional
+from typing import Optional, Any
 
 from frontmatter import Post
 
-from basic_memory.file_utils import has_frontmatter, remove_frontmatter, parse_frontmatter
+from basic_memory.file_utils import has_frontmatter, remove_frontmatter
 from basic_memory.markdown import EntityMarkdown
-from basic_memory.models import Entity
-from basic_memory.models import Observation as ObservationModel
+from basic_memory.models import Entity, Observation as ObservationModel
+from basic_memory.utils import generate_permalink
 
 
 def entity_model_from_markdown(
@@ -32,13 +32,16 @@ def entity_model_from_markdown(
     if not markdown.created or not markdown.modified:  # pragma: no cover
         raise ValueError("Both created and modified dates are required in markdown")
 
+    # Generate permalink if not provided
+    permalink = markdown.frontmatter.permalink or generate_permalink(file_path)
+
     # Create or update entity
     model = entity or Entity()
 
     # Update basic fields
     model.title = markdown.frontmatter.title
     model.entity_type = markdown.frontmatter.type
-    model.permalink = markdown.frontmatter.permalink
+    model.permalink = permalink
     model.file_path = str(file_path)
     model.content_type = "text/markdown"
     model.created_at = markdown.created
@@ -74,33 +77,22 @@ async def schema_to_markdown(schema: Any) -> Post:
     """
     # Extract content and metadata
     content = schema.content or ""
-    entity_metadata = dict(schema.entity_metadata or {})
+    frontmatter_metadata = dict(schema.entity_metadata or {})
 
     # if the content contains frontmatter, remove it and merge
     if has_frontmatter(content):
-        content_frontmatter = parse_frontmatter(content)
         content = remove_frontmatter(content)
 
-        # Merge content frontmatter with entity metadata
-        # (entity_metadata takes precedence for conflicts)
-        content_frontmatter.update(entity_metadata)
-        entity_metadata = content_frontmatter
-
     # Remove special fields for ordered frontmatter
     for field in ["type", "title", "permalink"]:
-        entity_metadata.pop(field, None)
+        frontmatter_metadata.pop(field, None)
 
-    # Create Post with fields ordered by insert order
+    # Create Post with ordered fields
     post = Post(
         content,
         title=schema.title,
         type=schema.entity_type,
+        permalink=schema.permalink,
+        **frontmatter_metadata,
     )
-    # set the permalink if passed in
-    if schema.permalink:
-        post.metadata["permalink"] = schema.permalink
-
-    if entity_metadata:
-        post.metadata.update(entity_metadata)
-
     return post

src/basic_memory/mcp/prompts/ai_assistant_guide.py

@@ -1,8 +1,9 @@
 from pathlib import Path
 
-from basic_memory.mcp.server import mcp
 from loguru import logger
 
+from basic_memory.mcp.server import mcp
+
 
 @mcp.resource(
     uri="memory://ai_assistant_guide",
@@ -19,7 +20,7 @@ def ai_assistant_guide() -> str:
         A focused guide on Basic Memory usage.
     """
     logger.info("Loading AI assistant guide resource")
-    guide_doc = Path(__file__).parent.parent / "resources" / "ai_assistant_guide.md"
-    content = guide_doc.read_text(encoding="utf-8")
+    guide_doc = Path(__file__).parent.parent.parent.parent.parent / "static" / "ai_assistant_guide.md"
+    content = guide_doc.read_text()
     logger.info(f"Loaded AI assistant guide ({len(content)} chars)")
     return content

src/basic_memory/mcp/prompts/continue_conversation.py

@@ -5,19 +5,19 @@ providing context from previous interactions to maintain continuity.
 """
 
 from textwrap import dedent
-from typing import Annotated, Optional
+from typing import Optional, Annotated
 
 from loguru import logger
 from pydantic import Field
 
-from basic_memory.mcp.prompts.utils import PromptContext, PromptContextItem, format_prompt_context
+from basic_memory.mcp.prompts.utils import format_prompt_context, PromptContext, PromptContextItem
 from basic_memory.mcp.server import mcp
 from basic_memory.mcp.tools.build_context import build_context
 from basic_memory.mcp.tools.recent_activity import recent_activity
-from basic_memory.mcp.tools.search import search_notes
+from basic_memory.mcp.tools.search import search
 from basic_memory.schemas.base import TimeFrame
 from basic_memory.schemas.memory import GraphContext
-from basic_memory.schemas.search import SearchItemType
+from basic_memory.schemas.search import SearchQuery, SearchItemType
 
 
 @mcp.prompt(
@@ -47,8 +47,8 @@ async def continue_conversation(
 
     # If topic provided, search for it
     if topic:
-        search_results = await search_notes(
-            query=topic, after_date=timeframe, entity_types=[SearchItemType.ENTITY]
+        search_results = await search(
+            SearchQuery(text=topic, after_date=timeframe, types=[SearchItemType.ENTITY])
         )
 
         # Build context from results
@@ -93,7 +93,7 @@ async def continue_conversation(
         ## Next Steps
 
         You can:
-        - Explore more with: `search_notes({{"text": "{topic}"}})`
+        - Explore more with: `search({{"text": "{topic}"}})`
         - See what's changed: `recent_activity(timeframe="{timeframe or "7d"}")`
         - **Record new learnings or decisions from this conversation:** `write_note(title="[Create a meaningful title]", content="[Content with observations and relations]")`
         

src/basic_memory/mcp/prompts/search.py

@@ -10,9 +10,9 @@ from loguru import logger
 from pydantic import Field
 
 from basic_memory.mcp.server import mcp
-from basic_memory.mcp.tools.search import search_notes as search_tool
+from basic_memory.mcp.tools.search import search as search_tool
 from basic_memory.schemas.base import TimeFrame
-from basic_memory.schemas.search import SearchResponse
+from basic_memory.schemas.search import SearchQuery, SearchResponse
 
 
 @mcp.prompt(
@@ -40,7 +40,7 @@ async def search_prompt(
     """
     logger.info(f"Searching knowledge base, query: {query}, timeframe: {timeframe}")
 
-    search_results = await search_tool(query=query, after_date=timeframe)
+    search_results = await search_tool(SearchQuery(text=query, after_date=timeframe))
     return format_search_results(query, search_results, timeframe)
 
 
@@ -144,9 +144,9 @@ def format_search_results(
         ## Next Steps
         
         You can:
-        - Refine your search: `search_notes("{query} AND additional_term")`
-        - Exclude terms: `search_notes("{query} NOT exclude_term")`
-        - View more results: `search_notes("{query}", after_date=None)`
+        - Refine your search: `search("{query} AND additional_term")`
+        - Exclude terms: `search("{query} NOT exclude_term")`
+        - View more results: `search("{query}", after_date=None)`
         - Check recent activity: `recent_activity()`
         
         ## Synthesize and Capture Knowledge

src/basic_memory/mcp/resources/ai_assistant_guide.md

@@ -1,413 +0,0 @@
-# AI Assistant Guide for Basic Memory
-
-This guide helps AIs use Basic Memory tools effectively when working with users. It covers reading, writing, and
-navigating knowledge through the Model Context Protocol (MCP).
-
-## Overview
-
-Basic Memory allows you and users to record context in local Markdown files, building a rich knowledge base through
-natural conversations. The system automatically creates a semantic knowledge graph from simple text patterns.
-
-- **Local-First**: All data is stored in plain text files on the user's computer
-- **Real-Time**: Users see content updates immediately
-- **Bi-Directional**: Both you and users can read and edit notes
-- **Semantic**: Simple patterns create a structured knowledge graph
-- **Persistent**: Knowledge persists across sessions and conversations
-
-## The Importance of the Knowledge Graph
-
-**Basic Memory's value comes from connections between notes, not just the notes themselves.**
-
-When writing notes, your primary goal should be creating a rich, interconnected knowledge graph:
-
-1. **Increase Semantic Density**: Add multiple observations and relations to each note
-2. **Use Accurate References**: Aim to reference existing entities by their exact titles
-3. **Create Forward References**: Feel free to reference entities that don't exist yet - Basic Memory will resolve these
-   when they're created later
-4. **Create Bidirectional Links**: When appropriate, connect entities from both directions
-5. **Use Meaningful Categories**: Add semantic context with appropriate observation categories
-6. **Choose Precise Relations**: Use specific relation types that convey meaning
-
-Remember: A knowledge graph with 10 heavily connected notes is more valuable than 20 isolated notes. Your job is to help
-build these connections!
-
-## Core Tools Reference
-
-```python
-# Writing knowledge - THE MOST IMPORTANT TOOL!
-response = await write_note(
-    title="Search Design",  # Required: Note title
-    content="# Search Design\n...",  # Required: Note content
-    folder="specs",  # Optional: Folder to save in
-    tags=["search", "design"],  # Optional: Tags for categorization
-    verbose=True  # Optional: Get parsing details
-)
-
-# Reading knowledge
-content = await read_note("Search Design")  # By title
-content = await read_note("specs/search-design")  # By path
-content = await read_note("memory://specs/search")  # By memory URL
-
-# Searching for knowledge
-results = await search_notes(
-    query="authentication system",  # Text to search for
-    page=1,  # Optional: Pagination
-    page_size=10  # Optional: Results per page
-)
-
-# Building context from the knowledge graph
-context = await build_context(
-    url="memory://specs/search",  # Starting point
-    depth=2,  # Optional: How many hops to follow
-    timeframe="1 month"  # Optional: Recent timeframe
-)
-
-# Checking recent changes
-activity = await recent_activity(
-    type="all",  # Optional: Entity types to include
-    depth=1,  # Optional: Related items to include
-    timeframe="1 week"  # Optional: Time window
-)
-
-# Creating a knowledge visualization
-canvas_result = await canvas(
-    nodes=[{"id": "note1", "label": "Search Design"}],  # Nodes to display
-    edges=[{"from": "note1", "to": "note2"}],  # Connections
-    title="Project Overview",  # Canvas title
-    folder="diagrams"  # Storage location
-)
-```
-
-## memory:// URLs Explained
-
-Basic Memory uses a special URL format to reference entities in the knowledge graph:
-
-- `memory://title` - Reference by title
-- `memory://folder/title` - Reference by folder and title
-- `memory://permalink` - Reference by permalink
-- `memory://path/relation_type/*` - Follow all relations of a specific type
-- `memory://path/*/target` - Find all entities with relations to target
-
-## Semantic Markdown Format
-
-Knowledge is encoded in standard markdown using simple patterns:
-
-**Observations** - Facts about an entity:
-
-```markdown
-- [category] This is an observation #tag1 #tag2 (optional context)
-```
-
-**Relations** - Links between entities:
-
-```markdown
-- relation_type [[Target Entity]] (optional context)
-```
-
-**Common Categories & Relation Types:**
-
-- Categories: `[idea]`, `[decision]`, `[question]`, `[fact]`, `[requirement]`, `[technique]`, `[recipe]`, `[preference]`
-- Relations: `relates_to`, `implements`, `requires`, `extends`, `part_of`, `pairs_with`, `inspired_by`,
-  `originated_from`
-
-## When to Record Context
-
-**Always consider recording context when**:
-
-1. Users make decisions or reach conclusions
-2. Important information emerges during conversation
-3. Multiple related topics are discussed
-4. The conversation contains information that might be useful later
-5. Plans, tasks, or action items are mentioned
-
-**Protocol for recording context**:
-
-1. Identify valuable information in the conversation
-2. Ask the user: "Would you like me to record our discussion about [topic] in Basic Memory?"
-3. If they agree, use `write_note` to capture the information
-4. If they decline, continue without recording
-5. Let the user know when information has been recorded: "I've saved our discussion about [topic] to Basic Memory."
-
-## Understanding User Interactions
-
-Users will interact with Basic Memory in patterns like:
-
-1. **Creating knowledge**:
-   ```
-   Human: "Let's write up what we discussed about search."
-   
-   You: I'll create a note capturing our discussion about the search functionality.
-   [Use write_note() to record the conversation details]
-   ```
-
-2. **Referencing existing knowledge**:
-   ```
-   Human: "Take a look at memory://specs/search"
-   
-   You: I'll examine that information.
-   [Use build_context() to gather related information]
-   [Then read_note() to access specific content]
-   ```
-
-3. **Finding information**:
-   ```
-   Human: "What were our decisions about auth?"
-   
-   You: Let me find that information for you.
-   [Use search_notes() to find relevant notes]
-   [Then build_context() to understand connections]
-   ```
-
-## Key Things to Remember
-
-1. **Files are Truth**
-    - All knowledge lives in local files on the user's computer
-    - Users can edit files outside your interaction
-    - Changes need to be synced by the user (usually automatic)
-    - Always verify information is current with `recent_activity()`
-
-2. **Building Context Effectively**
-    - Start with specific entities
-    - Follow meaningful relations
-    - Check recent changes
-    - Build context incrementally
-    - Combine related information
-
-3. **Writing Knowledge Wisely**
-    - Using the same title+folder will overwrite existing notes
-    - Structure content with clear headings and sections
-    - Use semantic markup for observations and relations
-    - Keep files organized in logical folders
-
-## Common Knowledge Patterns
-
-### Capturing Decisions
-
-```markdown
-# Coffee Brewing Methods
-
-## Context
-
-I've experimented with various brewing methods including French press, pour over, and espresso.
-
-## Decision
-
-Pour over is my preferred method for light to medium roasts because it highlights subtle flavors and offers more control
-over the extraction.
-
-## Observations
-
-- [technique] Blooming the coffee grounds for 30 seconds improves extraction #brewing
-- [preference] Water temperature between 195-205°F works best #temperature
-- [equipment] Gooseneck kettle provides better control of water flow #tools
-
-## Relations
-
-- pairs_with [[Light Roast Beans]]
-- contrasts_with [[French Press Method]]
-- requires [[Proper Grinding Technique]]
-```
-
-### Recording Project Structure
-
-```markdown
-# Garden Planning
-
-## Overview
-
-This document outlines the garden layout and planting strategy for this season.
-
-## Observations
-
-- [structure] Raised beds in south corner for sun exposure #layout
-- [structure] Drip irrigation system installed for efficiency #watering
-- [pattern] Companion planting used to deter pests naturally #technique
-
-## Relations
-
-- contains [[Vegetable Section]]
-- contains [[Herb Garden]]
-- implements [[Organic Gardening Principles]]
-```
-
-### Technical Discussions
-
-```markdown
-# Recipe Improvement Discussion
-
-## Key Points
-
-Discussed strategies for improving the chocolate chip cookie recipe.
-
-## Observations
-
-- [issue] Cookies spread too thin when baked at 350°F #texture
-- [solution] Chilling dough for 24 hours improves flavor and reduces spreading #technique
-- [decision] Will use brown butter instead of regular butter #flavor
-
-## Relations
-
-- improves [[Basic Cookie Recipe]]
-- inspired_by [[Bakery-Style Cookies]]
-- pairs_with [[Homemade Ice Cream]]
-```
-
-### Creating Effective Relations
-
-When creating relations, you can:
-
-1. Reference existing entities by their exact title
-2. Create forward references to entities that don't exist yet
-
-```python
-# Example workflow for creating notes with effective relations
-async def create_note_with_effective_relations():
-    # Search for existing entities to reference
-    search_results = await search_notes("travel")
-    existing_entities = [result.title for result in search_results.primary_results]
-
-    # Check if specific entities exist
-    packing_tips_exists = "Packing Tips" in existing_entities
-    japan_travel_exists = "Japan Travel Guide" in existing_entities
-
-    # Prepare relations section - include both existing and forward references
-    relations_section = "## Relations\n"
-
-    # Existing reference - exact match to known entity
-    if packing_tips_exists:
-        relations_section += "- references [[Packing Tips]]\n"
-    else:
-        # Forward reference - will be linked when that entity is created later
-        relations_section += "- references [[Packing Tips]]\n"
-
-    # Another possible reference
-    if japan_travel_exists:
-        relations_section += "- part_of [[Japan Travel Guide]]\n"
-
-    # You can also check recently modified notes to reference them
-    recent = await recent_activity(timeframe="1 week")
-    recent_titles = [item.title for item in recent.primary_results]
-
-    if "Transportation Options" in recent_titles:
-        relations_section += "- relates_to [[Transportation Options]]\n"
-
-    # Always include meaningful forward references, even if they don't exist yet
-    relations_section += "- located_in [[Tokyo]]\n"
-    relations_section += "- visited_during [[Spring 2023 Trip]]\n"
-
-    # Now create the note with both verified and forward relations
-    content = f"""# Tokyo Neighborhood Guide
-    
-## Overview
-Details about different Tokyo neighborhoods and their unique characteristics.
-
-## Observations
-- [area] Shibuya is a busy shopping district #shopping
-- [transportation] Yamanote Line connects major neighborhoods #transit
-- [recommendation] Visit Shimokitazawa for vintage shopping #unique
-- [tip] Get a Suica card for easy train travel #convenience
-
-{relations_section}
-    """
-
-    result = await write_note(
-        title="Tokyo Neighborhood Guide",
-        content=content,
-        verbose=True
-    )
-
-    # You can check which relations were resolved and which are forward references
-    if result and 'relations' in result:
-        resolved = [r['to_name'] for r in result['relations'] if r.get('target_id')]
-        forward_refs = [r['to_name'] for r in result['relations'] if not r.get('target_id')]
-
-        print(f"Resolved relations: {resolved}")
-        print(f"Forward references that will be resolved later: {forward_refs}")
-```
-
-## Error Handling
-
-Common issues to watch for:
-
-1. **Missing Content**
-   ```python
-   try:
-       content = await read_note("Document")
-   except:
-       # Try search instead
-       results = await search_notes("Document")
-       if results and results.primary_results:
-           # Found something similar
-           content = await read_note(results.primary_results[0].permalink)
-   ```
-
-2. **Forward References (Unresolved Relations)**
-   ```python
-   response = await write_note(..., verbose=True)
-   # Check for forward references (unresolved relations)
-   forward_refs = []
-   for relation in response.get('relations', []):
-       if not relation.get('target_id'):
-           forward_refs.append(relation.get('to_name'))
-   
-   if forward_refs:
-       # This is a feature, not an error! Inform the user about forward references
-       print(f"Note created with forward references to: {forward_refs}")
-       print("These will be automatically linked when those notes are created.")
-       
-       # Optionally suggest creating those entities now
-       print("Would you like me to create any of these notes now to complete the connections?")
-   ```
-
-3. **Sync Issues**
-   ```python
-   # If information seems outdated
-   activity = await recent_activity(timeframe="1 hour")
-   if not activity or not activity.primary_results:
-       print("It seems there haven't been recent updates. You might need to run 'basic-memory sync'.")
-   ```
-
-## Best Practices
-
-1. **Proactively Record Context**
-    - Offer to capture important discussions
-    - Record decisions, rationales, and conclusions
-    - Link to related topics
-    - Ask for permission first: "Would you like me to save our discussion about [topic]?"
-    - Confirm when complete: "I've saved our discussion to Basic Memory"
-
-2. **Create a Rich Semantic Graph**
-    - **Add meaningful observations**: Include at least 3-5 categorized observations in each note
-    - **Create deliberate relations**: Connect each note to at least 2-3 related entities
-    - **Use existing entities**: Before creating a new relation, search for existing entities
-    - **Verify wikilinks**: When referencing `[[Entity]]`, use exact titles of existing notes
-    - **Check accuracy**: Use `search_notes()` or `recent_activity()` to confirm entity titles
-    - **Use precise relation types**: Choose specific relation types that convey meaning (e.g., "implements" instead
-      of "relates_to")
-    - **Consider bidirectional relations**: When appropriate, create inverse relations in both entities
-
-3. **Structure Content Thoughtfully**
-    - Use clear, descriptive titles
-    - Organize with logical sections (Context, Decision, Implementation, etc.)
-    - Include relevant context and background
-    - Add semantic observations with appropriate categories
-    - Use a consistent format for similar types of notes
-    - Balance detail with conciseness
-
-4. **Navigate Knowledge Effectively**
-    - Start with specific searches
-    - Follow relation paths
-    - Combine information from multiple sources
-    - Verify information is current
-    - Build a complete picture before responding
-
-5. **Help Users Maintain Their Knowledge**
-    - Suggest organizing related topics
-    - Identify potential duplicates
-    - Recommend adding relations between topics
-    - Offer to create summaries of scattered information
-    - Suggest potential missing relations: "I notice this might relate to [topic], would you like me to add that
-      connection?"
-
-Built with ♥️ b
-y Basic Machines

src/basic_memory/mcp/server.py

@@ -1,37 +1,11 @@
 """Enhanced FastMCP server instance for Basic Memory."""
 
-import asyncio
-from contextlib import asynccontextmanager
-from typing import AsyncIterator, Optional
-
 from mcp.server.fastmcp import FastMCP
-from mcp.server.fastmcp.utilities.logging import configure_logging as mcp_configure_logging
-from dataclasses import dataclass
-
-from basic_memory.config import config as project_config
-from basic_memory.services.initialization import initialize_app
+from mcp.server.fastmcp.utilities.logging import configure_logging
 
 # mcp console logging
-mcp_configure_logging(level="ERROR")
-
-
-@dataclass
-class AppContext:
-    watch_task: Optional[asyncio.Task]
-
-
-@asynccontextmanager
-async def app_lifespan(server: FastMCP) -> AsyncIterator[AppContext]:  # pragma: no cover
-    """Manage application lifecycle with type-safe context"""
-    # Initialize on startup
-    watch_task = await initialize_app(project_config)
-    try:
-        yield AppContext(watch_task=watch_task)
-    finally:
-        # Cleanup on shutdown
-        if watch_task:
-            watch_task.cancel()
+configure_logging(level="INFO")
 
 
 # Create the shared server instance
-mcp = FastMCP("Basic Memory", log_level="ERROR", lifespan=app_lifespan)
+mcp = FastMCP("Basic Memory")

src/basic_memory/mcp/tools/__init__.py

@@ -12,7 +12,7 @@ from basic_memory.mcp.tools.build_context import build_context
 from basic_memory.mcp.tools.recent_activity import recent_activity
 from basic_memory.mcp.tools.read_note import read_note
 from basic_memory.mcp.tools.write_note import write_note
-from basic_memory.mcp.tools.search import search_notes
+from basic_memory.mcp.tools.search import search
 from basic_memory.mcp.tools.canvas import canvas
 
 __all__ = [
@@ -22,6 +22,6 @@ __all__ = [
     "read_content",
     "read_note",
     "recent_activity",
-    "search_notes",
+    "search",
     "write_note",
 ]

src/basic_memory/mcp/tools/read_note.py

@@ -6,9 +6,10 @@ from loguru import logger
 
 from basic_memory.mcp.async_client import client
 from basic_memory.mcp.server import mcp
-from basic_memory.mcp.tools.search import search_notes
+from basic_memory.mcp.tools.search import search
 from basic_memory.mcp.tools.utils import call_get
 from basic_memory.schemas.memory import memory_url_path
+from basic_memory.schemas.search import SearchQuery
 
 
 @mcp.tool(
@@ -62,7 +63,7 @@ async def read_note(identifier: str, page: int = 1, page_size: int = 10) -> str:
 
     # Fallback 1: Try title search via API
     logger.info(f"Search title for: {identifier}")
-    title_results = await search_notes(query=identifier, search_type="title")
+    title_results = await search(SearchQuery(title=identifier))
 
     if title_results and title_results.results:
         result = title_results.results[0]  # Get the first/best match
@@ -86,7 +87,7 @@ async def read_note(identifier: str, page: int = 1, page_size: int = 10) -> str:
 
     # Fallback 2: Text search as a last resort
     logger.info(f"Title search failed, trying text search for: {identifier}")
-    text_results = await search_notes(query=identifier, search_type="text")
+    text_results = await search(SearchQuery(text=identifier))
 
     # We didn't find a direct match, construct a helpful error message
     if not text_results or not text_results.results:
@@ -111,7 +112,7 @@ def format_not_found_message(identifier: str) -> str:
         ## Search Instead
         Try searching for related content:
         ```
-        search_notes(query="{identifier}")
+        search(query="{identifier}")
         ```
         
         ## Recent Activity
@@ -172,7 +173,7 @@ def format_related_results(identifier: str, results) -> str:
         ## Search For More Results
         To see more related content:
         ```
-        search_notes(query="{identifier}")
+        search(query="{identifier}")
         ```
         
         ## Create New Note

src/basic_memory/mcp/tools/recent_activity.py

@@ -1,6 +1,6 @@
 """Recent activity tool for Basic Memory MCP server."""
 
-from typing import List, Union
+from typing import Optional, List
 
 from loguru import logger
 
@@ -14,7 +14,7 @@ from basic_memory.schemas.search import SearchItemType
 
 @mcp.tool(
     description="""Get recent activity from across the knowledge base.
-
+    
     Timeframe supports natural language formats like:
     - "2 days ago"  
     - "last week"
@@ -25,9 +25,9 @@ from basic_memory.schemas.search import SearchItemType
     """,
 )
 async def recent_activity(
-    type: Union[str, List[str]] = "",
-    depth: int = 1,
-    timeframe: TimeFrame = "7d",
+    type: Optional[List[SearchItemType]] = None,
+    depth: Optional[int] = 1,
+    timeframe: Optional[TimeFrame] = "7d",
     page: int = 1,
     page_size: int = 10,
     max_related: int = 10,
@@ -35,14 +35,11 @@ async def recent_activity(
     """Get recent activity across the knowledge base.
 
     Args:
-        type: Filter by content type(s). Can be a string or list of strings.
-            Valid options:
-            - "entity" or ["entity"] for knowledge entities
-            - "relation" or ["relation"] for connections between entities
-            - "observation" or ["observation"] for notes and observations
+        type: Filter by content type(s). Valid options:
+            - ["entity"] for knowledge entities
+            - ["relation"] for connections between entities
+            - ["observation"] for notes and observations
             Multiple types can be combined: ["entity", "relation"]
-            Case-insensitive: "ENTITY" and "entity" are treated the same.
-            Default is an empty string, which returns all types.
         depth: How many relation hops to traverse (1-3 recommended)
         timeframe: Time window to search. Supports natural language:
             - Relative: "2 days ago", "last week", "yesterday"
@@ -62,17 +59,14 @@ async def recent_activity(
         # Get all entities for the last 10 days (default)
         recent_activity()
 
-        # Get all entities from yesterday (string format)
-        recent_activity(type="entity", timeframe="yesterday")
-
-        # Get all entities from yesterday (list format)
+        # Get all entities from yesterday
         recent_activity(type=["entity"], timeframe="yesterday")
 
         # Get recent relations and observations
         recent_activity(type=["relation", "observation"], timeframe="today")
 
         # Look back further with more context
-        recent_activity(type="entity", depth=2, timeframe="2 weeks ago")
+        recent_activity(type=["entity"], depth=2, timeframe="2 weeks ago")
 
     Notes:
         - Higher depth values (>3) may impact performance with large result sets
@@ -92,27 +86,11 @@ async def recent_activity(
     if timeframe:
         params["timeframe"] = timeframe  # pyright: ignore
 
-    # Validate and convert type parameter
+    # send enum values if we have an enum, else send string value
     if type:
-        # Convert single string to list
-        if isinstance(type, str):
-            type_list = [type]
-        else:
-            type_list = type
-
-        # Validate each type against SearchItemType enum
-        validated_types = []
-        for t in type_list:
-            try:
-                # Try to convert string to enum
-                if isinstance(t, str):
-                    validated_types.append(SearchItemType(t.lower()))
-            except ValueError:
-                valid_types = [t.value for t in SearchItemType]
-                raise ValueError(f"Invalid type: {t}. Valid types are: {valid_types}")
-
-        # Add validated types to params
-        params["type"] = [t.value for t in validated_types]  # pyright: ignore
+        params["type"] = [  # pyright: ignore
+            type.value if isinstance(type, SearchItemType) else type for type in type
+        ]
 
     response = await call_get(
         client,

src/basic_memory/mcp/tools/search.py

@@ -1,113 +1,77 @@
 """Search tools for Basic Memory MCP server."""
 
-from typing import List, Optional
-
 from loguru import logger
 
-from basic_memory.mcp.async_client import client
 from basic_memory.mcp.server import mcp
 from basic_memory.mcp.tools.utils import call_post
-from basic_memory.schemas.search import SearchItemType, SearchQuery, SearchResponse
+from basic_memory.schemas.search import SearchQuery, SearchResponse
+from basic_memory.mcp.async_client import client
 
 
 @mcp.tool(
-    description="Search across all content in the knowledge base.",
+    description="Search across all content in basic-memory, including documents and entities",
 )
-async def search_notes(
-    query: str,
-    page: int = 1,
-    page_size: int = 10,
-    search_type: str = "text",
-    types: Optional[List[str]] = None,
-    entity_types: Optional[List[str]] = None,
-    after_date: Optional[str] = None,
-) -> SearchResponse:
-    """Search across all content in the knowledge base.
+async def search(query: SearchQuery, page: int = 1, page_size: int = 10) -> SearchResponse:
+    """Search across all content in basic-memory.
 
     This tool searches the knowledge base using full-text search, pattern matching,
     or exact permalink lookup. It supports filtering by content type, entity type,
     and date.
 
     Args:
-        query: The search query string
+        query: SearchQuery object with search parameters including:
+            - text: Full-text search (e.g., "project planning")
+              Supports boolean operators: AND, OR, NOT and parentheses for grouping
+            - title: Search only in titles (e.g., "Meeting notes")
+            - permalink: Exact permalink match (e.g., "docs/meeting-notes")
+            - permalink_match: Pattern matching for permalinks (e.g., "docs/*-notes")
+            - types: Optional list of content types to search (e.g., ["entity", "observation"])
+            - entity_types: Optional list of entity types to filter by (e.g., ["note", "person"])
+            - after_date: Optional date filter for recent content (e.g., "1 week", "2d")
         page: The page number of results to return (default 1)
         page_size: The number of results to return per page (default 10)
-        search_type: Type of search to perform, one of: "text", "title", "permalink" (default: "text")
-        types: Optional list of note types to search (e.g., ["note", "person"])
-        entity_types: Optional list of entity types to filter by (e.g., ["entity", "observation"])
-        after_date: Optional date filter for recent content (e.g., "1 week", "2d")
 
     Returns:
         SearchResponse with results and pagination info
 
     Examples:
         # Basic text search
-        results = await search_notes("project planning")
+        results = await search(SearchQuery(text="project planning"))
 
         # Boolean AND search (both terms must be present)
-        results = await search_notes("project AND planning")
+        results = await search(SearchQuery(text="project AND planning"))
 
         # Boolean OR search (either term can be present)
-        results = await search_notes("project OR meeting")
+        results = await search(SearchQuery(text="project OR meeting"))
 
         # Boolean NOT search (exclude terms)
-        results = await search_notes("project NOT meeting")
+        results = await search(SearchQuery(text="project NOT meeting"))
 
         # Boolean search with grouping
-        results = await search_notes("(project OR planning) AND notes")
+        results = await search(SearchQuery(text="(project OR planning) AND notes"))
 
         # Search with type filter
-        results = await search_notes(
-            query="meeting notes",
+        results = await search(SearchQuery(
+            text="meeting notes",
             types=["entity"],
-        )
-
-        # Search with entity type filter, e.g., note vs
-        results = await search_notes(
-            query="meeting notes",
-            types=["entity"],
-        )
+        ))
 
         # Search for recent content
-        results = await search_notes(
-            query="bug report",
+        results = await search(SearchQuery(
+            text="bug report",
             after_date="1 week"
-        )
+        ))
 
         # Pattern matching on permalinks
-        results = await search_notes(
-            query="docs/meeting-*",
-            search_type="permalink"
-        )
+        results = await search(SearchQuery(
+            permalink_match="docs/meeting-*"
+        ))
     """
-    # Create a SearchQuery object based on the parameters
-    search_query = SearchQuery()
-
-    # Set the appropriate search field based on search_type
-    if search_type == "text":
-        search_query.text = query
-    elif search_type == "title":
-        search_query.title = query
-    elif search_type == "permalink" and "*" in query:
-        search_query.permalink_match = query
-    elif search_type == "permalink":
-        search_query.permalink = query
-    else:
-        search_query.text = query  # Default to text search
-
-    # Add optional filters if provided
-    if entity_types:
-        search_query.entity_types = [SearchItemType(t) for t in entity_types]
-    if types:
-        search_query.types = types
-    if after_date:
-        search_query.after_date = after_date
-
-    logger.info(f"Searching for {search_query}")
+    logger.info(f"Searching for {query}")
     response = await call_post(
         client,
         "/search/",
-        json=search_query.model_dump(),
+        json=query.model_dump(),
         params={"page": page, "page_size": page_size},
     )
     return SearchResponse.model_validate(response.json())

src/basic_memory/mcp/tools/write_note.py

@@ -1,6 +1,6 @@
 """Write note tool for Basic Memory MCP server."""
 
-from typing import List, Union
+from typing import Optional, List
 
 from loguru import logger
 
@@ -9,13 +9,6 @@ from basic_memory.mcp.server import mcp
 from basic_memory.mcp.tools.utils import call_put
 from basic_memory.schemas import EntityResponse
 from basic_memory.schemas.base import Entity
-from basic_memory.utils import parse_tags
-
-# Define TagType as a Union that can accept either a string or a list of strings or None
-TagType = Union[List[str], str, None]
-
-# Define TagType as a Union that can accept either a string or a list of strings or None
-TagType = Union[List[str], str, None]
 
 
 @mcp.tool(
@@ -25,7 +18,7 @@ async def write_note(
     title: str,
     content: str,
     folder: str,
-    tags=None,  # Remove type hint completely to avoid schema issues
+    tags: Optional[List[str]] = None,
 ) -> str:
     """Write a markdown note to the knowledge base.
 
@@ -47,14 +40,13 @@ async def write_note(
         Examples:
         `- depends_on [[Content Parser]] (Need for semantic extraction)`
         `- implements [[Search Spec]] (Initial implementation)`
-        `- This feature extends [[Base Design]] andst uses [[Core Utils]]`
+        `- This feature extends [[Base Design]] and uses [[Core Utils]]`
 
     Args:
         title: The title of the note
         content: Markdown content for the note, can include observations and relations
         folder: the folder where the file should be saved
-        tags: Tags to categorize the note. Can be a list of strings, a comma-separated string, or None.
-              Note: If passing from external MCP clients, use a string format (e.g. "tag1,tag2,tag3")
+        tags: Optional list of tags to categorize the note
 
     Returns:
         A markdown formatted summary of the semantic content, including:
@@ -66,10 +58,8 @@ async def write_note(
     """
     logger.info("MCP tool call", tool="write_note", folder=folder, title=title, tags=tags)
 
-    # Process tags using the helper function
-    tag_list = parse_tags(tags)
     # Create the entity request
-    metadata = {"tags": [f"#{tag}" for tag in tag_list]} if tag_list else None
+    metadata = {"tags": [f"#{tag}" for tag in tags]} if tags else None
     entity = Entity(
         title=title,
         folder=folder,
@@ -88,10 +78,8 @@ async def write_note(
     # Format semantic summary based on status code
     action = "Created" if response.status_code == 201 else "Updated"
     summary = [
-        f"# {action} note",
-        f"file_path: {result.file_path}",
+        f"# {action} {result.file_path} ({result.checksum[:8] if result.checksum else 'unknown'})",
         f"permalink: {result.permalink}",
-        f"checksum: {result.checksum[:8] if result.checksum else 'unknown'}",
     ]
 
     # Count observations by category
@@ -117,8 +105,8 @@ async def write_note(
             summary.append(f"- Unresolved: {unresolved}")
             summary.append("\nUnresolved relations will be retried on next sync.")
 
-    if tag_list:
-        summary.append(f"\n## Tags\n- {', '.join(tag_list)}")
+    if tags:
+        summary.append(f"\n## Tags\n- {', '.join(tags)}")
 
     # Log the response with structured data
     logger.info(

src/basic_memory/repository/repository.py

@@ -137,6 +137,8 @@ class Repository[T: Base]:
 
     async def find_one(self, query: Select[tuple[T]]) -> Optional[T]:
         """Execute a query and retrieve a single record."""
+        logger.debug(f"Finding one {self.Model.__name__} with query: {query}")
+
         # add in load options
         query = query.options(*self.get_load_options())
         result = await self.execute_query(query)
@@ -268,9 +270,11 @@ class Repository[T: Base]:
         """Execute a query asynchronously."""
 
         query = query.options(*self.get_load_options()) if use_query_options else query
+
         logger.debug(f"Executing query: {query}")
         async with db.scoped_session(self.session_maker) as session:
             result = await session.execute(query)
+            logger.debug("Query executed successfully")
             return result
 
     def get_load_options(self) -> List[LoaderOption]:

src/basic_memory/repository/search_repository.py

@@ -4,10 +4,10 @@ import json
 import time
 from dataclasses import dataclass
 from datetime import datetime
-from typing import Any, Dict, List, Optional
+from typing import List, Optional, Any, Dict
 
 from loguru import logger
-from sqlalchemy import Executable, Result, text
+from sqlalchemy import text, Executable, Result
 from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker
 
 from basic_memory import db
@@ -123,9 +123,9 @@ class SearchRepository:
         permalink: Optional[str] = None,
         permalink_match: Optional[str] = None,
         title: Optional[str] = None,
-        types: Optional[List[str]] = None,
+        types: Optional[List[SearchItemType]] = None,
         after_date: Optional[datetime] = None,
-        entity_types: Optional[List[SearchItemType]] = None,
+        entity_types: Optional[List[str]] = None,
         limit: int = 10,
         offset: int = 0,
     ) -> List[SearchIndexRow]:
@@ -174,15 +174,15 @@ class SearchRepository:
             else:
                 conditions.append("permalink MATCH :permalink")
 
-        # Handle entity type filter
-        if entity_types:
-            type_list = ", ".join(f"'{t.value}'" for t in entity_types)
-            conditions.append(f"type IN ({type_list})")
-
         # Handle type filter
         if types:
-            type_list = ", ".join(f"'{t}'" for t in types)
-            conditions.append(f"json_extract(metadata, '$.entity_type') IN ({type_list})")
+            type_list = ", ".join(f"'{t.value}'" for t in types)
+            conditions.append(f"type IN ({type_list})")
+
+        # Handle entity type filter
+        if entity_types:
+            entity_type_list = ", ".join(f"'{t}'" for t in entity_types)
+            conditions.append(f"json_extract(metadata, '$.entity_type') IN ({entity_type_list})")
 
         # Handle date filter using datetime() for proper comparison
         if after_date:

src/basic_memory/schemas/search.py

@@ -49,8 +49,8 @@ class SearchQuery(BaseModel):
     title: Optional[str] = None  # title only search
 
     # Optional filters
-    types: Optional[List[str]] = None  # Filter by type
-    entity_types: Optional[List[SearchItemType]] = None  # Filter by entity type
+    types: Optional[List[SearchItemType]] = None  # Filter by item type
+    entity_types: Optional[List[str]] = None  # Filter by entity type
     after_date: Optional[Union[datetime, str]] = None  # Time-based filter
 
     @field_validator("after_date")

src/basic_memory/services/context_service.py

@@ -81,7 +81,7 @@ class ContextService:
         else:
             logger.debug(f"Build context for '{types}'")
             primary = await self.search_repository.search(
-                entity_types=types, after_date=since, limit=limit, offset=offset
+                types=types, after_date=since, limit=limit, offset=offset
             )
 
         # Get type_id pairs for traversal

src/basic_memory/services/entity_service.py

@@ -1,24 +1,24 @@
 """Service for managing entities in the database."""
 
 from pathlib import Path
-from typing import List, Optional, Sequence, Tuple, Union
+from typing import Sequence, List, Optional, Tuple, Union
 
 import frontmatter
 from loguru import logger
 from sqlalchemy.exc import IntegrityError
 
 from basic_memory.markdown import EntityMarkdown
-from basic_memory.markdown.entity_parser import EntityParser
 from basic_memory.markdown.utils import entity_model_from_markdown, schema_to_markdown
-from basic_memory.models import Entity as EntityModel
-from basic_memory.models import Observation, Relation
+from basic_memory.models import Entity as EntityModel, Observation, Relation
 from basic_memory.repository import ObservationRepository, RelationRepository
 from basic_memory.repository.entity_repository import EntityRepository
 from basic_memory.schemas import Entity as EntitySchema
 from basic_memory.schemas.base import Permalink
-from basic_memory.services import BaseService, FileService
-from basic_memory.services.exceptions import EntityCreationError, EntityNotFoundError
+from basic_memory.services.exceptions import EntityNotFoundError, EntityCreationError
+from basic_memory.services import FileService
+from basic_memory.services import BaseService
 from basic_memory.services.link_resolver import LinkResolver
+from basic_memory.markdown.entity_parser import EntityParser
 from basic_memory.utils import generate_permalink
 
 
@@ -89,7 +89,7 @@ class EntityService(BaseService[EntityModel]):
         logger.debug(f"Creating or updating entity: {schema}")
 
         # Try to find existing entity using smart resolution
-        existing = await self.link_resolver.resolve_link(schema.permalink or schema.file_path)
+        existing = await self.link_resolver.resolve_link(schema.permalink)
 
         if existing:
             logger.debug(f"Found existing entity: {existing.permalink}")
@@ -100,7 +100,7 @@ class EntityService(BaseService[EntityModel]):
 
     async def create_entity(self, schema: EntitySchema) -> EntityModel:
         """Create a new entity and write to filesystem."""
-        logger.debug(f"Creating entity: {schema.title}")
+        logger.debug(f"Creating entity: {schema.permalink}")
 
         # Get file path and ensure it's a Path object
         file_path = Path(schema.file_path)
@@ -141,20 +141,10 @@ class EntityService(BaseService[EntityModel]):
         # Convert file path string to Path
         file_path = Path(entity.file_path)
 
-        # Read existing frontmatter from the file if it exists
-        existing_markdown = await self.entity_parser.parse_file(file_path)
-
-        # Create post with new content from schema
         post = await schema_to_markdown(schema)
 
-        # Merge new metadata with existing metadata
-        existing_markdown.frontmatter.metadata.update(post.metadata)
-
-        # Create a new post with merged metadata
-        merged_post = frontmatter.Post(post.content, **existing_markdown.frontmatter.metadata)
-
         # write file
-        final_content = frontmatter.dumps(merged_post, sort_keys=False)
+        final_content = frontmatter.dumps(post, sort_keys=False)
         checksum = await self.file_service.write_file(file_path, final_content)
 
         # parse entity from file
@@ -230,7 +220,7 @@ class EntityService(BaseService[EntityModel]):
         Creates the entity with null checksum to indicate sync not complete.
         Relations will be added in second pass.
         """
-        logger.debug(f"Creating entity: {markdown.frontmatter.title} file_path: {file_path}")
+        logger.debug(f"Creating entity: {markdown.frontmatter.title}")
         model = entity_model_from_markdown(file_path, markdown)
 
         # Mark as incomplete because we still need to add relations
@@ -315,7 +305,7 @@ class EntityService(BaseService[EntityModel]):
             except IntegrityError:
                 # Unique constraint violation - relation already exists
                 logger.debug(
-                    f"Skipping duplicate relation {rel.type} from {db_entity.permalink} target: {rel.target}"
+                    f"Skipping duplicate relation {rel.type} from {db_entity.permalink} target: {rel.target}, type: {rel.type}"
                 )
                 continue
 

src/basic_memory/services/file_service.py

@@ -5,6 +5,8 @@ from os import stat_result
 from pathlib import Path
 from typing import Any, Dict, Tuple, Union
 
+from loguru import logger
+
 from basic_memory import file_utils
 from basic_memory.file_utils import FileError
 from basic_memory.markdown.markdown_processor import MarkdownProcessor
@@ -12,7 +14,6 @@ from basic_memory.models import Entity as EntityModel
 from basic_memory.schemas import Entity as EntitySchema
 from basic_memory.services.exceptions import FileOperationError
 from basic_memory.utils import FilePath
-from loguru import logger
 
 
 class FileService:
@@ -60,7 +61,7 @@ class FileService:
         Returns:
             Raw content string without metadata sections
         """
-        logger.debug(f"Reading entity content, entity_id={entity.id}, permalink={entity.permalink}")
+        logger.debug("Reading entity content", entity_id=entity.id, permalink=entity.permalink)
 
         file_path = self.get_entity_path(entity)
         markdown = await self.markdown_processor.read_file(file_path)
@@ -170,7 +171,8 @@ class FileService:
 
         try:
             logger.debug("Reading file", operation="read_file", path=str(full_path))
-            content = full_path.read_text(encoding="utf-8")
+
+            content = full_path.read_text()
             checksum = await file_utils.compute_checksum(content)
 
             logger.debug(
@@ -234,7 +236,7 @@ class FileService:
         try:
             if self.is_markdown(path):
                 # read str
-                content = full_path.read_text(encoding="utf-8")
+                content = full_path.read_text()
             else:
                 # read bytes
                 content = full_path.read_bytes()

src/basic_memory/services/initialization.py

@@ -1,143 +0,0 @@
-"""Shared initialization service for Basic Memory.
-
-This module provides shared initialization functions used by both CLI and API
-to ensure consistent application startup across all entry points.
-"""
-
-import asyncio
-from typing import Optional
-
-from loguru import logger
-
-from basic_memory import db
-from basic_memory.config import ProjectConfig, config_manager
-from basic_memory.sync import WatchService
-
-# Import this inside functions to avoid circular imports
-# from basic_memory.cli.commands.sync import get_sync_service
-
-
-async def initialize_database(app_config: ProjectConfig) -> None:
-    """Run database migrations to ensure schema is up to date.
-
-    Args:
-        app_config: The Basic Memory project configuration
-    """
-    try:
-        logger.info("Running database migrations...")
-        await db.run_migrations(app_config)
-        logger.info("Migrations completed successfully")
-    except Exception as e:
-        logger.error(f"Error running migrations: {e}")
-        # Allow application to continue - it might still work
-        # depending on what the error was, and will fail with a
-        # more specific error if the database is actually unusable
-
-
-async def initialize_file_sync(
-    app_config: ProjectConfig,
-) -> asyncio.Task:
-    """Initialize file synchronization services.
-
-    Args:
-        app_config: The Basic Memory project configuration
-
-    Returns:
-        Tuple of (sync_service, watch_service, watch_task) if sync is enabled,
-        or (None, None, None) if sync is disabled
-    """
-    # Load app configuration
-    # Import here to avoid circular imports
-    from basic_memory.cli.commands.sync import get_sync_service
-
-    # Initialize sync service
-    sync_service = await get_sync_service()
-
-    # Initialize watch service
-    watch_service = WatchService(
-        sync_service=sync_service,
-        file_service=sync_service.entity_service.file_service,
-        config=app_config,
-        quiet=True,
-    )
-
-    # Create the background task for running sync
-    async def run_background_sync():  # pragma: no cover
-        # Run initial full sync
-        await sync_service.sync(app_config.home)
-        logger.info("Sync completed successfully")
-
-        # Start background sync task
-        logger.info(f"Starting watch service to sync file changes in dir: {app_config.home}")
-
-        # Start watching for changes
-        await watch_service.run()
-
-    watch_task = asyncio.create_task(run_background_sync())
-    logger.info("Watch service started")
-    return watch_task
-
-
-async def initialize_app(
-    app_config: ProjectConfig,
-) -> Optional[asyncio.Task]:
-    """Initialize the Basic Memory application.
-
-    This function handles all initialization steps needed for both API and shor lived CLI commands.
-    For long running commands like mcp, a
-    - Running database migrations
-    - Setting up file synchronization
-
-    Args:
-        app_config: The Basic Memory project configuration
-    """
-    # Initialize database first
-    await initialize_database(app_config)
-
-    basic_memory_config = config_manager.load_config()
-    logger.info(f"Sync changes enabled: {basic_memory_config.sync_changes}")
-    logger.info(
-        f"Update permalinks on move enabled: {basic_memory_config.update_permalinks_on_move}"
-    )
-    if not basic_memory_config.sync_changes:  # pragma: no cover
-        logger.info("Sync changes disabled. Skipping watch service.")
-        return
-
-    # Initialize file sync services
-    return await initialize_file_sync(app_config)
-
-
-def ensure_initialization(app_config: ProjectConfig) -> None:
-    """Ensure initialization runs in a synchronous context.
-
-    This is a wrapper for the async initialize_app function that can be
-    called from synchronous code like CLI entry points.
-
-    Args:
-        app_config: The Basic Memory project configuration
-    """
-    try:
-        asyncio.run(initialize_app(app_config))
-    except Exception as e:
-        logger.error(f"Error during initialization: {e}")
-        # Continue execution even if initialization fails
-        # The command might still work, or will fail with a
-        # more specific error message
-
-
-def ensure_initialize_database(app_config: ProjectConfig) -> None:
-    """Ensure initialization runs in a synchronous context.
-
-    This is a wrapper for the async initialize_database function that can be
-    called from synchronous code like CLI entry points.
-
-    Args:
-        app_config: The Basic Memory project configuration
-    """
-    try:
-        asyncio.run(initialize_database(app_config))
-    except Exception as e:
-        logger.error(f"Error during initialization: {e}")
-        # Continue execution even if initialization fails
-        # The command might still work, or will fail with a
-        # more specific error message

src/basic_memory/services/link_resolver.py

@@ -46,17 +46,10 @@ class LinkResolver:
             logger.debug(f"Found title match: {entity.title}")
             return entity
 
-        # 3. Try file path
-        found_path = await self.entity_repository.get_by_file_path(clean_text)
-        if found_path:
-            logger.debug(f"Found entity with path: {found_path.file_path}")
-            return found_path
-
-        # search if indicated
         if use_search and "*" not in clean_text:
             # 3. Fall back to search for fuzzy matching on title
             results = await self.search_service.search(
-                query=SearchQuery(title=clean_text, entity_types=[SearchItemType.ENTITY]),
+                query=SearchQuery(title=clean_text, types=[SearchItemType.ENTITY]),
             )
 
             if results:

src/basic_memory/services/search_service.py

@@ -181,6 +181,17 @@ class SearchService:
         Each type gets its own row in the search index with appropriate metadata.
         """
 
+        if entity.permalink is None:  # pragma: no cover
+            logger.error(
+                "Missing permalink for markdown entity",
+                entity_id=entity.id,
+                title=entity.title,
+                file_path=entity.file_path,
+            )
+            raise ValueError(
+                f"Entity permalink should not be None for markdown entity: {entity.id} ({entity.title})"
+            )
+
         content_stems = []
         content_snippet = ""
         title_variants = self._generate_variants(entity.title)
@@ -191,13 +202,22 @@ class SearchService:
             content_stems.append(content)
             content_snippet = f"{content[:250]}"
 
-        if entity.permalink:
-            content_stems.extend(self._generate_variants(entity.permalink))
-
+        content_stems.extend(self._generate_variants(entity.permalink))
         content_stems.extend(self._generate_variants(entity.file_path))
 
         entity_content_stems = "\n".join(p for p in content_stems if p and p.strip())
 
+        if entity.permalink is None:  # pragma: no cover
+            logger.error(
+                "Missing permalink for markdown entity",
+                entity_id=entity.id,
+                title=entity.title,
+                file_path=entity.file_path,
+            )
+            raise ValueError(
+                f"Entity permalink should not be None for markdown entity: {entity.id} ({entity.title})"
+            )
+
         # Index entity
         await self.repository.index_item(
             SearchIndexRow(

src/basic_memory/sync/sync_service.py

@@ -1,8 +1,9 @@
 """Service for syncing files between filesystem and database."""
 
 import os
-import time
-from dataclasses import dataclass, field
+
+from dataclasses import dataclass
+from dataclasses import field
 from datetime import datetime
 from pathlib import Path
 from typing import Dict, Optional, Set, Tuple
@@ -10,13 +11,13 @@ from typing import Dict, Optional, Set, Tuple
 from loguru import logger
 from sqlalchemy.exc import IntegrityError
 
-from basic_memory.config import ProjectConfig
-from basic_memory.file_utils import has_frontmatter
 from basic_memory.markdown import EntityParser
 from basic_memory.models import Entity
 from basic_memory.repository import EntityRepository, RelationRepository
 from basic_memory.services import EntityService, FileService
 from basic_memory.services.search_service import SearchService
+import time
+from rich.progress import Progress, TextColumn, BarColumn, TaskProgressColumn
 
 
 @dataclass
@@ -64,7 +65,6 @@ class SyncService:
 
     def __init__(
         self,
-        config: ProjectConfig,
         entity_service: EntityService,
         entity_parser: EntityParser,
         entity_repository: EntityRepository,
@@ -72,7 +72,6 @@ class SyncService:
         search_service: SearchService,
         file_service: FileService,
     ):
-        self.config = config
         self.entity_service = entity_service
         self.entity_parser = entity_parser
         self.entity_repository = entity_repository
@@ -80,51 +79,145 @@ class SyncService:
         self.search_service = search_service
         self.file_service = file_service
 
-    async def sync(self, directory: Path) -> SyncReport:
+    async def sync(self, directory: Path, show_progress: bool = True) -> SyncReport:
         """Sync all files with database."""
 
         start_time = time.time()
-        logger.info(f"Sync operation started for directory: {directory}")
+        console = None
+        progress = None  # Will be initialized if show_progress is True
+
+        logger.info("Sync operation started", directory=str(directory))
 
         # initial paths from db to sync
         # path -> checksum
+        if show_progress:
+            from rich.console import Console
+
+            console = Console()
+            console.print(f"Scanning directory: {directory}")
+
         report = await self.scan(directory)
 
         # Initialize progress tracking if requested
+        if show_progress and report.total > 0:
+            progress = Progress(
+                TextColumn("[bold blue]{task.description}"),
+                BarColumn(),
+                TaskProgressColumn(),
+                console=console,
+                expand=True,
+            )
+
         # order of sync matters to resolve relations effectively
         logger.info(
-            f"Sync changes detected: new_files={len(report.new)}, modified_files={len(report.modified)}, "
-            + f"deleted_files={len(report.deleted)}, moved_files={len(report.moves)}"
+            "Sync changes detected",
+            new_files=len(report.new),
+            modified_files=len(report.modified),
+            deleted_files=len(report.deleted),
+            moved_files=len(report.moves),
         )
 
-        # sync moves first
-        for old_path, new_path in report.moves.items():
-            # in the case where a file has been deleted and replaced by another file
-            # it will show up in the move and modified lists, so handle it in modified
-            if new_path in report.modified:
-                report.modified.remove(new_path)
-                logger.debug(
-                    f"File marked as moved and modified: old_path={old_path}, new_path={new_path}"
+        if show_progress and report.total > 0:
+            with progress:  # pyright: ignore
+                # Track each category separately
+                move_task = None
+                if report.moves:  # pragma: no cover
+                    move_task = progress.add_task("[blue]Moving files...", total=len(report.moves))  # pyright: ignore
+
+            delete_task = None
+            if report.deleted:  # pragma: no cover
+                delete_task = progress.add_task(  # pyright: ignore
+                    "[red]Deleting files...", total=len(report.deleted)
                 )
-            else:
-                await self.handle_move(old_path, new_path)
 
-        # deleted next
-        for path in report.deleted:
-            await self.handle_delete(path)
+            new_task = None
+            if report.new:
+                new_task = progress.add_task(  # pyright: ignore
+                    "[green]Adding new files...", total=len(report.new)
+                )
 
-        # then new and modified
-        for path in report.new:
-            await self.sync_file(path, new=True)
+            modify_task = None
+            if report.modified:  # pragma: no cover
+                modify_task = progress.add_task(  # pyright: ignore
+                    "[yellow]Updating modified files...", total=len(report.modified)
+                )
 
-        for path in report.modified:
-            await self.sync_file(path, new=False)
+            # sync moves first
+            for i, (old_path, new_path) in enumerate(report.moves.items()):
+                # in the case where a file has been deleted and replaced by another file
+                # it will show up in the move and modified lists, so handle it in modified
+                if new_path in report.modified:  # pragma: no cover
+                    report.modified.remove(new_path)
+                    logger.debug(
+                        "File marked as moved and modified",
+                        old_path=old_path,
+                        new_path=new_path,
+                        action="processing as modified",
+                    )
+                else:  # pragma: no cover
+                    await self.handle_move(old_path, new_path)
 
-        await self.resolve_relations()
+                if move_task is not None:  # pragma: no cover
+                    progress.update(move_task, advance=1)  # pyright: ignore
+
+            # deleted next
+            for i, path in enumerate(report.deleted):  # pragma: no cover
+                await self.handle_delete(path)
+                if delete_task is not None:  # pragma: no cover
+                    progress.update(delete_task, advance=1)  # pyright: ignore
+
+            # then new and modified
+            for i, path in enumerate(report.new):
+                await self.sync_file(path, new=True)
+                if new_task is not None:
+                    progress.update(new_task, advance=1)  # pyright: ignore
+
+            for i, path in enumerate(report.modified):  # pragma: no cover
+                await self.sync_file(path, new=False)
+                if modify_task is not None:  # pragma: no cover
+                    progress.update(modify_task, advance=1)  # pyright: ignore
+
+            # Final step - resolving relations
+            if report.total > 0:
+                relation_task = progress.add_task("[cyan]Resolving relations...", total=1)  # pyright: ignore
+                await self.resolve_relations()
+                progress.update(relation_task, advance=1)  # pyright: ignore
+        else:
+            # No progress display - proceed with normal sync
+            # sync moves first
+            for old_path, new_path in report.moves.items():
+                # in the case where a file has been deleted and replaced by another file
+                # it will show up in the move and modified lists, so handle it in modified
+                if new_path in report.modified:
+                    report.modified.remove(new_path)
+                    logger.debug(
+                        "File marked as moved and modified",
+                        old_path=old_path,
+                        new_path=new_path,
+                        action="processing as modified",
+                    )
+                else:
+                    await self.handle_move(old_path, new_path)
+
+            # deleted next
+            for path in report.deleted:
+                await self.handle_delete(path)
+
+            # then new and modified
+            for path in report.new:
+                await self.sync_file(path, new=True)
+
+            for path in report.modified:
+                await self.sync_file(path, new=False)
+
+            await self.resolve_relations()
 
         duration_ms = int((time.time() - start_time) * 1000)
         logger.info(
-            f"Sync operation completed: directory={directory}, total_changes={report.total}, duration_ms={duration_ms}"
+            "Sync operation completed",
+            directory=str(directory),
+            total_changes=report.total,
+            duration_ms=duration_ms,
         )
 
         return report
@@ -133,7 +226,6 @@ class SyncService:
         """Scan directory for changes compared to database state."""
 
         db_paths = await self.get_db_file_state()
-        logger.debug(f"Found {len(db_paths)} db paths")
 
         # Track potentially moved files by checksum
         scan_result = await self.scan_directory(directory)
@@ -184,7 +276,6 @@ class SyncService:
             :param db_records: the data from the db
         """
         db_records = await self.entity_repository.find_all()
-        logger.info(f"Found {len(db_records)} db records")
         return {r.file_path: r.checksum or "" for r in db_records}
 
     async def sync_file(
@@ -201,7 +292,10 @@ class SyncService:
         """
         try:
             logger.debug(
-                f"Syncing file path={path} is_new={new} is_markdown={self.file_service.is_markdown(path)}"
+                "Syncing file",
+                path=path,
+                is_new=new,
+                is_markdown=self.file_service.is_markdown(path),
             )
 
             if self.file_service.is_markdown(path):
@@ -213,7 +307,7 @@ class SyncService:
                 await self.search_service.index_entity(entity)
 
                 logger.debug(
-                    f"File sync completed, path={path}, entity_id={entity.id}, checksum={checksum[:8]}"
+                    "File sync completed", path=path, entity_id=entity.id, checksum=checksum
                 )
             return entity, checksum
 
@@ -232,59 +326,54 @@ class SyncService:
             Tuple of (entity, checksum)
         """
         # Parse markdown first to get any existing permalink
-        logger.debug(f"Parsing markdown file, path: {path}, new: {new}")
-
-        file_path = self.entity_parser.base_path / path
-        file_content = file_path.read_text(encoding="utf-8")
-        file_contains_frontmatter = has_frontmatter(file_content)
-
-        # entity markdown will always contain front matter, so it can be used up create/update the entity
+        logger.debug("Parsing markdown file", path=path)
         entity_markdown = await self.entity_parser.parse_file(path)
 
-        # if the file contains frontmatter, resolve a permalink
-        if file_contains_frontmatter:
-            # Resolve permalink - this handles all the cases including conflicts
-            permalink = await self.entity_service.resolve_permalink(path, markdown=entity_markdown)
+        # Resolve permalink - this handles all the cases including conflicts
+        permalink = await self.entity_service.resolve_permalink(path, markdown=entity_markdown)
 
-            # If permalink changed, update the file
-            if permalink != entity_markdown.frontmatter.permalink:
-                logger.info(
-                    f"Updating permalink for path: {path}, old_permalink: {entity_markdown.frontmatter.permalink}, new_permalink: {permalink}"
-                )
+        # If permalink changed, update the file
+        if permalink != entity_markdown.frontmatter.permalink:
+            logger.info(
+                "Updating permalink",
+                path=path,
+                old_permalink=entity_markdown.frontmatter.permalink,
+                new_permalink=permalink,
+            )
 
-                entity_markdown.frontmatter.metadata["permalink"] = permalink
-                await self.file_service.update_frontmatter(path, {"permalink": permalink})
+            entity_markdown.frontmatter.metadata["permalink"] = permalink
+            checksum = await self.file_service.update_frontmatter(path, {"permalink": permalink})
+        else:
+            checksum = await self.file_service.compute_checksum(path)
 
         # if the file is new, create an entity
         if new:
             # Create entity with final permalink
-            logger.debug(f"Creating new entity from markdown, path={path}")
+            logger.debug("Creating new entity from markdown", path=path, permalink=permalink)
+
             await self.entity_service.create_entity_from_markdown(Path(path), entity_markdown)
 
         # otherwise we need to update the entity and observations
         else:
-            logger.debug(f"Updating entity from markdown, path={path}")
+            logger.debug("Updating entity from markdown", path=path, permalink=permalink)
+
             await self.entity_service.update_entity_and_observations(Path(path), entity_markdown)
 
         # Update relations and search index
         entity = await self.entity_service.update_entity_relations(path, entity_markdown)
 
-        # After updating relations, we need to compute the checksum again
-        # This is necessary for files with wikilinks to ensure consistent checksums
-        # after relation processing is complete
-        final_checksum = await self.file_service.compute_checksum(path)
-
         # set checksum
-        await self.entity_repository.update(entity.id, {"checksum": final_checksum})
+        await self.entity_repository.update(entity.id, {"checksum": checksum})
 
         logger.debug(
-            f"Markdown sync completed: path={path}, entity_id={entity.id}, "
-            f"observation_count={len(entity.observations)}, relation_count={len(entity.relations)}, "
-            f"checksum={final_checksum[:8]}"
+            "Markdown sync completed",
+            path=path,
+            entity_id=entity.id,
+            observation_count=len(entity.observations),
+            relation_count=len(entity.relations),
         )
 
-        # Return the final checksum to ensure everything is consistent
-        return entity, final_checksum
+        return entity, checksum
 
     async def sync_regular_file(self, path: str, new: bool = True) -> Tuple[Optional[Entity], str]:
         """Sync a non-markdown file with basic tracking.
@@ -325,7 +414,7 @@ class SyncService:
         else:
             entity = await self.entity_repository.get_by_file_path(path)
             if entity is None:  # pragma: no cover
-                logger.error(f"Entity not found for existing file, path={path}")
+                logger.error("Entity not found for existing file", path=path)
                 raise ValueError(f"Entity not found for existing file: {path}")
 
             updated = await self.entity_repository.update(
@@ -333,7 +422,7 @@ class SyncService:
             )
 
             if updated is None:  # pragma: no cover
-                logger.error(f"Failed to update entity, entity_id={entity.id}, path={path}")
+                logger.error("Failed to update entity", entity_id=entity.id, path=path)
                 raise ValueError(f"Failed to update entity with ID {entity.id}")
 
             return updated, checksum
@@ -345,7 +434,10 @@ class SyncService:
         entity = await self.entity_repository.get_by_file_path(file_path)
         if entity:
             logger.info(
-                f"Deleting entity with file_path={file_path}, entity_id={entity.id}, permalink={entity.permalink}"
+                "Deleting entity",
+                file_path=file_path,
+                entity_id=entity.id,
+                permalink=entity.permalink,
             )
 
             # Delete from db (this cascades to observations/relations)
@@ -359,8 +451,10 @@ class SyncService:
             )
 
             logger.debug(
-                f"Cleaning up search index for entity_id={entity.id}, file_path={file_path}, "
-                f"index_entries={len(permalinks)}"
+                "Cleaning up search index",
+                entity_id=entity.id,
+                file_path=file_path,
+                index_entries=len(permalinks),
             )
 
             for permalink in permalinks:
@@ -370,49 +464,28 @@ class SyncService:
                     await self.search_service.delete_by_entity_id(entity.id)
 
     async def handle_move(self, old_path, new_path):
-        logger.debug("Moving entity", old_path=old_path, new_path=new_path)
+        logger.info("Moving entity", old_path=old_path, new_path=new_path)
 
         entity = await self.entity_repository.get_by_file_path(old_path)
         if entity:
-            # Update file_path in all cases
-            updates = {"file_path": new_path}
-
-            # If configured, also update permalink to match new path
-            if self.config.update_permalinks_on_move:
-                # generate new permalink value
-                new_permalink = await self.entity_service.resolve_permalink(new_path)
-
-                # write to file and get new checksum
-                new_checksum = await self.file_service.update_frontmatter(
-                    new_path, {"permalink": new_permalink}
-                )
-
-                updates["permalink"] = new_permalink
-                updates["checksum"] = new_checksum
-
-                logger.info(
-                    f"Updating permalink on move,old_permalink={entity.permalink}"
-                    f"new_permalink={new_permalink}"
-                    f"new_checksum={new_checksum}"
-                )
-
-            updated = await self.entity_repository.update(entity.id, updates)
+            # Update file_path but keep the same permalink for link stability
+            updated = await self.entity_repository.update(entity.id, {"file_path": new_path})
 
             if updated is None:  # pragma: no cover
                 logger.error(
-                    "Failed to update entity path"
-                    f"entity_id={entity.id}"
-                    f"old_path={old_path}"
-                    f"new_path={new_path}"
+                    "Failed to update entity path",
+                    entity_id=entity.id,
+                    old_path=old_path,
+                    new_path=new_path,
                 )
                 raise ValueError(f"Failed to update entity path for ID {entity.id}")
 
             logger.debug(
-                "Entity path updated"
-                f"entity_id={entity.id} "
-                f"permalink={entity.permalink} "
-                f"old_path={old_path} "
-                f"new_path={new_path} "
+                "Entity path updated",
+                entity_id=entity.id,
+                permalink=entity.permalink,
+                old_path=old_path,
+                new_path=new_path,
             )
 
             # update search index
@@ -427,10 +500,10 @@ class SyncService:
 
         for relation in unresolved_relations:
             logger.debug(
-                "Attempting to resolve relation "
-                f"relation_id={relation.id} "
-                f"from_id={relation.from_id} "
-                f"to_name={relation.to_name}"
+                "Attempting to resolve relation",
+                relation_id=relation.id,
+                from_id=relation.from_id,
+                to_name=relation.to_name,
             )
 
             resolved_entity = await self.entity_service.link_resolver.resolve_link(relation.to_name)
@@ -438,12 +511,12 @@ class SyncService:
             # ignore reference to self
             if resolved_entity and resolved_entity.id != relation.from_id:
                 logger.debug(
-                    "Resolved forward reference "
-                    f"relation_id={relation.id} "
-                    f"from_id={relation.from_id} "
-                    f"to_name={relation.to_name} "
-                    f"resolved_id={resolved_entity.id} "
-                    f"resolved_title={resolved_entity.title}",
+                    "Resolved forward reference",
+                    relation_id=relation.id,
+                    from_id=relation.from_id,
+                    to_name=relation.to_name,
+                    resolved_id=resolved_entity.id,
+                    resolved_title=resolved_entity.title,
                 )
                 try:
                     await self.relation_repository.update(
@@ -455,10 +528,10 @@ class SyncService:
                     )
                 except IntegrityError:  # pragma: no cover
                     logger.debug(
-                        "Ignoring duplicate relation "
-                        f"relation_id={relation.id} "
-                        f"from_id={relation.from_id} "
-                        f"to_name={relation.to_name}"
+                        "Ignoring duplicate relation",
+                        relation_id=relation.id,
+                        from_id=relation.from_id,
+                        to_name=relation.to_name,
                     )
 
                 # update search index
@@ -476,7 +549,7 @@ class SyncService:
         """
         start_time = time.time()
 
-        logger.debug(f"Scanning directory {directory}")
+        logger.debug("Scanning directory", directory=str(directory))
         result = ScanResult()
 
         for root, dirnames, filenames in os.walk(str(directory)):
@@ -498,10 +571,10 @@ class SyncService:
 
         duration_ms = int((time.time() - start_time) * 1000)
         logger.debug(
-            f"{directory} scan completed "
-            f"directory={str(directory)} "
-            f"files_found={len(result.files)} "
-            f"duration_ms={duration_ms}"
+            "Directory scan completed",
+            directory=str(directory),
+            files_found=len(result.files),
+            duration_ms=duration_ms,
         )
 
         return result

src/basic_memory/sync/watch_service.py

@@ -5,15 +5,16 @@ from datetime import datetime
 from pathlib import Path
 from typing import List, Optional, Set
 
-from basic_memory.config import ProjectConfig
-from basic_memory.services.file_service import FileService
-from basic_memory.sync.sync_service import SyncService
 from loguru import logger
 from pydantic import BaseModel
 from rich.console import Console
 from watchfiles import awatch
 from watchfiles.main import FileChange, Change
 
+from basic_memory.config import ProjectConfig
+from basic_memory.services.file_service import FileService
+from basic_memory.sync.sync_service import SyncService
+
 WATCH_STATUS_JSON = "watch-status.json"
 
 
@@ -70,30 +71,22 @@ class WatchServiceState(BaseModel):
 
 
 class WatchService:
-    def __init__(
-        self,
-        sync_service: SyncService,
-        file_service: FileService,
-        config: ProjectConfig,
-        quiet: bool = False,
-    ):
+    def __init__(self, sync_service: SyncService, file_service: FileService, config: ProjectConfig):
         self.sync_service = sync_service
         self.file_service = file_service
         self.config = config
         self.state = WatchServiceState()
         self.status_path = config.home / ".basic-memory" / WATCH_STATUS_JSON
         self.status_path.parent.mkdir(parents=True, exist_ok=True)
-
-        # quiet mode for mcp so it doesn't mess up stdout
-        self.console = Console(quiet=quiet)
+        self.console = Console()
 
     async def run(self):  # pragma: no cover
         """Watch for file changes and sync them"""
         logger.info(
             "Watch service started",
-            f"directory={str(self.config.home)}",
-            f"debounce_ms={self.config.sync_delay}",
-            f"pid={os.getpid()}",
+            directory=str(self.config.home),
+            debounce_ms=self.config.sync_delay,
+            pid=os.getpid(),
         )
 
         self.state.running = True
@@ -119,8 +112,8 @@ class WatchService:
         finally:
             logger.info(
                 "Watch service stopped",
-                f"directory={str(self.config.home)}",
-                f"runtime_seconds={int((datetime.now() - self.state.start_time).total_seconds())}",
+                directory=str(self.config.home),
+                runtime_seconds=int((datetime.now() - self.state.start_time).total_seconds()),
             )
 
             self.state.running = False
@@ -145,10 +138,6 @@ class WatchService:
             if part.startswith("."):
                 return False
 
-        # Skip temp files used in atomic operations
-        if path.endswith(".tmp"):
-            return False
-
         return True
 
     async def write_status(self):
@@ -162,7 +151,7 @@ class WatchService:
 
         start_time = time.time()
 
-        logger.info(f"Processing file changes, change_count={len(changes)}, directory={directory}")
+        logger.info("Processing file changes", change_count=len(changes), directory=str(directory))
 
         # Group changes by type
         adds: List[str] = []
@@ -172,11 +161,6 @@ class WatchService:
         for change, path in changes:
             # convert to relative path
             relative_path = str(Path(path).relative_to(directory))
-
-            # Skip .tmp files - they're temporary and shouldn't be synced
-            if relative_path.endswith(".tmp"):
-                continue
-
             if change == Change.added:
                 adds.append(relative_path)
             elif change == Change.deleted:
@@ -185,17 +169,9 @@ class WatchService:
                 modifies.append(relative_path)
 
         logger.debug(
-            f"Grouped file changes, added={len(adds)}, deleted={len(deletes)}, modified={len(modifies)}"
+            "Grouped file changes", added=len(adds), deleted=len(deletes), modified=len(modifies)
         )
 
-        # because of our atomic writes on updates, an add may be an existing file
-        for added_path in adds:  # pragma: no cover TODO add test
-            entity = await self.sync_service.entity_repository.get_by_file_path(added_path)
-            if entity is not None:
-                logger.debug(f"Existing file will be processed as modified, path={added_path}")
-                adds.remove(added_path)
-                modifies.append(added_path)
-
         # Track processed files to avoid duplicates
         processed: Set[str] = set()
 
@@ -208,8 +184,8 @@ class WatchService:
             # We don't need to process directories, only the files inside them
             # This prevents errors when trying to compute checksums or read directories as files
             added_full_path = directory / added_path
-            if not added_full_path.exists() or added_full_path.is_dir():
-                logger.debug("Skipping non-existent or directory path", path=added_path)
+            if added_full_path.is_dir():
+                logger.debug("Skipping directory for move detection", path=added_path)
                 processed.add(added_path)
                 continue
 
@@ -239,16 +215,15 @@ class WatchService:
                                 status="success",
                             )
                             self.console.print(f"[blue]→[/blue] {deleted_path} → {added_path}")
-                            logger.info(f"move: {deleted_path} -> {added_path}")
                             processed.add(added_path)
                             processed.add(deleted_path)
                             break
                     except Exception as e:  # pragma: no cover
                         logger.warning(
                             "Error checking for move",
-                            f"old_path={deleted_path}",
-                            f"new_path={added_path}",
-                            f"error={str(e)}",
+                            old_path=deleted_path,
+                            new_path=added_path,
+                            error=str(e),
                         )
 
         # Handle remaining changes - group them by type for concise output
@@ -264,7 +239,6 @@ class WatchService:
                 await self.sync_service.handle_delete(path)
                 self.state.add_event(path=path, action="deleted", status="success")
                 self.console.print(f"[red]✕[/red] {path}")
-                logger.info(f"deleted: {path}")
                 processed.add(path)
                 delete_count += 1
 
@@ -273,29 +247,28 @@ class WatchService:
             if path not in processed:
                 # Skip directories - only process files
                 full_path = directory / path
-                if not full_path.exists() or full_path.is_dir():
-                    logger.debug(
-                        f"Skipping non-existent or directory path, path={path}"
-                    )  # pragma: no cover
-                    processed.add(path)  # pragma: no cover
-                    continue  # pragma: no cover
+                if full_path.is_dir():  # pragma: no cover
+                    logger.debug("Skipping directory", path=path)
+                    processed.add(path)
+                    continue
 
-                logger.debug(f"Processing new file, path={path}")
+                logger.debug("Processing new file", path=path)
                 entity, checksum = await self.sync_service.sync_file(path, new=True)
                 if checksum:
                     self.state.add_event(
                         path=path, action="new", status="success", checksum=checksum
                     )
                     self.console.print(f"[green]✓[/green] {path}")
-                    logger.info(
-                        "new file processed",
-                        f"path={path}",
-                        f"checksum={checksum}",
+                    logger.debug(
+                        "Added file processed",
+                        path=path,
+                        entity_id=entity.id if entity else None,
+                        checksum=checksum,
                     )
                     processed.add(path)
                     add_count += 1
                 else:  # pragma: no cover
-                    logger.warning(f"Error syncing new file, path={path}")  # pragma: no cover
+                    logger.warning("Error syncing new file", path=path)  # pragma: no cover
                     self.console.print(
                         f"[orange]?[/orange] Error syncing: {path}"
                     )  # pragma: no cover
@@ -308,12 +281,12 @@ class WatchService:
             if path not in processed:
                 # Skip directories - only process files
                 full_path = directory / path
-                if not full_path.exists() or full_path.is_dir():
-                    logger.debug("Skipping non-existent or directory path", path=path)
+                if full_path.is_dir():
+                    logger.debug("Skipping directory", path=path)
                     processed.add(path)
                     continue
 
-                logger.debug(f"Processing modified file: path={path}")
+                logger.debug("Processing modified file", path=path)
                 entity, checksum = await self.sync_service.sync_file(path, new=False)
                 self.state.add_event(
                     path=path, action="modified", status="success", checksum=checksum
@@ -328,18 +301,17 @@ class WatchService:
                             f"[yellow]...[/yellow] Repeated changes to {path}"
                         )  # pragma: no cover
                 else:
-                    # haven't processed this file
+                    # New file being modified
                     self.console.print(f"[yellow]✎[/yellow] {path}")
-                    logger.info(f"modified: {path}")
                     last_modified_path = path
                     repeat_count = 0
                     modify_count += 1
 
                 logger.debug(
-                    "Modified file processed, "
-                    f"path={path} "
-                    f"entity_id={entity.id if entity else None} "
-                    f"checksum={checksum}",
+                    "Modified file processed",
+                    path=path,
+                    entity_id=entity.id if entity else None,
+                    checksum=checksum,
                 )
                 processed.add(path)
 
@@ -357,17 +329,16 @@ class WatchService:
 
             if changes:
                 self.console.print(f"{', '.join(changes)}", style="dim")  # pyright: ignore
-                logger.info(f"changes: {len(changes)}")
 
         duration_ms = int((time.time() - start_time) * 1000)
         self.state.last_scan = datetime.now()
         self.state.synced_files += len(processed)
 
         logger.info(
-            "File change processing completed, "
-            f"processed_files={len(processed)}, "
-            f"total_synced_files={self.state.synced_files}, "
-            f"duration_ms={duration_ms}"
+            "File change processing completed",
+            processed_files=len(processed),
+            total_synced_files=self.state.synced_files,
+            duration_ms=duration_ms,
         )
 
         await self.write_status()

src/basic_memory/utils.py

@@ -5,11 +5,11 @@ import os
 import logging
 import re
 import sys
-import unicodedata
 from pathlib import Path
-from typing import Optional, Protocol, Union, runtime_checkable, List, Any
+from typing import Optional, Protocol, Union, runtime_checkable
 
 from loguru import logger
+from unidecode import unidecode
 
 
 @runtime_checkable
@@ -27,23 +27,23 @@ FilePath = Union[Path, str]
 logging.getLogger("opentelemetry.sdk.metrics._internal.instrument").setLevel(logging.ERROR)
 
 
-def generate_permalink(file_path: Union[Path, str, Any]) -> str:
-    """
-    Generate a permalink from a file path.
+def generate_permalink(file_path: Union[Path, str, PathLike]) -> str:
+    """Generate a stable permalink from a file path.
+
+    Args:
+        file_path: Original file path (str, Path, or PathLike)
 
     Returns:
         Normalized permalink that matches validation rules. Converts spaces and underscores
-        to hyphens for consistency. Preserves non-ASCII characters like Chinese.
+        to hyphens for consistency.
 
     Examples:
         >>> generate_permalink("docs/My Feature.md")
         'docs/my-feature'
-        >>> generate_permalink("specs/API_v2.md")
+        >>> generate_permalink("specs/API (v2).md")
         'specs/api-v2'
         >>> generate_permalink("design/unified_model_refactor.md")
         'design/unified-model-refactor'
-        >>> generate_permalink("中文/测试文档.md")
-        '中文/测试文档'
     """
     # Convert Path to string if needed
     path_str = str(file_path)
@@ -51,74 +51,24 @@ def generate_permalink(file_path: Union[Path, str, Any]) -> str:
     # Remove extension
     base = os.path.splitext(path_str)[0]
 
-    # Create a transliteration mapping for specific characters
-    transliteration_map = {
-        "ø": "o",  # Handle Søren -> soren
-        "å": "a",  # Handle Kierkegård -> kierkegard
-        "ü": "u",  # Handle Müller -> muller
-        "é": "e",  # Handle Café -> cafe
-        "è": "e",  # Handle Mère -> mere
-        "ê": "e",  # Handle Fête -> fete
-        "à": "a",  # Handle À la mode -> a la mode
-        "ç": "c",  # Handle Façade -> facade
-        "ñ": "n",  # Handle Niño -> nino
-        "ö": "o",  # Handle Björk -> bjork
-        "ä": "a",  # Handle Häagen -> haagen
-        # Add more mappings as needed
-    }
-
-    # Process character by character, transliterating Latin characters with diacritics
-    result = ""
-    for char in base:
-        # Direct mapping for known characters
-        if char.lower() in transliteration_map:
-            result += transliteration_map[char.lower()]
-        # General case using Unicode normalization
-        elif unicodedata.category(char).startswith("L") and ord(char) > 127:
-            # Decompose the character (e.g., ü -> u + combining diaeresis)
-            decomposed = unicodedata.normalize("NFD", char)
-            # If decomposition produced multiple characters and first one is ASCII
-            if len(decomposed) > 1 and ord(decomposed[0]) < 128:
-                # Keep only the base character
-                result += decomposed[0].lower()
-            else:
-                # For non-Latin scripts like Chinese, preserve the character
-                result += char
-        else:
-            # Add the character as is
-            result += char
-
-    # Handle special punctuation cases for apostrophes
-    result = result.replace("'", "")
+    # Transliterate unicode to ascii
+    ascii_text = unidecode(base)
 
     # Insert dash between camelCase
-    # This regex finds boundaries between lowercase and uppercase letters
-    result = re.sub(r"([a-z0-9])([A-Z])", r"\1-\2", result)
+    ascii_text = re.sub(r"([a-z0-9])([A-Z])", r"\1-\2", ascii_text)
 
-    # Insert dash between Chinese and Latin character boundaries
-    # This is needed for cases like "中文English" -> "中文-english"
-    result = re.sub(r"([\u4e00-\u9fff])([a-zA-Z])", r"\1-\2", result)
-    result = re.sub(r"([a-zA-Z])([\u4e00-\u9fff])", r"\1-\2", result)
+    # Convert to lowercase
+    lower_text = ascii_text.lower()
 
-    # Convert ASCII letters to lowercase, preserve non-ASCII characters
-    lower_text = "".join(c.lower() if c.isascii() and c.isalpha() else c for c in result)
-
-    # Replace underscores with hyphens
+    # replace underscores with hyphens
     text_with_hyphens = lower_text.replace("_", "-")
 
-    # Replace spaces and unsafe ASCII characters with hyphens, but preserve non-ASCII characters
-    # Include common Chinese character ranges and other non-ASCII characters
-    clean_text = re.sub(
-        r"[^a-z0-9\u4e00-\u9fff\u3000-\u303f\u3400-\u4dbf/\-]", "-", text_with_hyphens
-    )
+    # Replace remaining invalid chars with hyphens
+    clean_text = re.sub(r"[^a-z0-9/\-]", "-", text_with_hyphens)
 
     # Collapse multiple hyphens
     clean_text = re.sub(r"-+", "-", clean_text)
 
-    # Remove hyphens between adjacent Chinese characters only
-    # This handles cases like "你好-世界" -> "你好世界"
-    clean_text = re.sub(r"([\u4e00-\u9fff])-([\u4e00-\u9fff])", r"\1\2", clean_text)
-
     # Clean each path segment
     segments = clean_text.split("/")
     clean_segments = [s.strip("-") for s in segments]
@@ -178,37 +128,3 @@ def setup_logging(
     # Set log levels for noisy loggers
     for logger_name, level in noisy_loggers.items():
         logging.getLogger(logger_name).setLevel(level)
-
-
-def parse_tags(tags: Union[List[str], str, None]) -> List[str]:
-    """Parse tags from various input formats into a consistent list.
-
-    Args:
-        tags: Can be a list of strings, a comma-separated string, or None
-
-    Returns:
-        A list of tag strings, or an empty list if no tags
-
-    Note:
-        This function strips leading '#' characters from tags to prevent
-        their accumulation when tags are processed multiple times.
-    """
-    if tags is None:
-        return []
-
-    # Process list of tags
-    if isinstance(tags, list):
-        # First strip whitespace, then strip leading '#' characters to prevent accumulation
-        return [tag.strip().lstrip("#") for tag in tags if tag and tag.strip()]
-
-    # Process comma-separated string of tags
-    if isinstance(tags, str):
-        # Split by comma, strip whitespace, then strip leading '#' characters
-        return [tag.strip().lstrip("#") for tag in tags.split(",") if tag and tag.strip()]
-
-    # For any other type, try to convert to string and parse
-    try:  # pragma: no cover
-        return parse_tags(str(tags))
-    except (ValueError, TypeError):  # pragma: no cover
-        logger.warning(f"Couldn't parse tags from input of type {type(tags)}: {tags}")
-        return []

static/ai_assistant_guide.md

@@ -49,7 +49,7 @@ content = await read_note("specs/search-design")  # By path
 content = await read_note("memory://specs/search")  # By memory URL
 
 # Searching for knowledge
-results = await search_notes(
+results = await search(
     query="authentication system",  # Text to search for
     page=1,  # Optional: Pagination
     page_size=10  # Optional: Results per page
@@ -154,7 +154,7 @@ Users will interact with Basic Memory in patterns like:
    Human: "What were our decisions about auth?"
    
    You: Let me find that information for you.
-   [Use search_notes() to find relevant notes]
+   [Use search() to find relevant notes]
    [Then build_context() to understand connections]
    ```
 
@@ -263,7 +263,7 @@ When creating relations, you can:
 # Example workflow for creating notes with effective relations
 async def create_note_with_effective_relations():
     # Search for existing entities to reference
-    search_results = await search_notes("travel")
+    search_results = await search("travel")
     existing_entities = [result.title for result in search_results.primary_results]
 
     # Check if specific entities exist
@@ -335,7 +335,7 @@ Common issues to watch for:
        content = await read_note("Document")
    except:
        # Try search instead
-       results = await search_notes("Document")
+       results = await search("Document")
        if results and results.primary_results:
            # Found something similar
            content = await read_note(results.primary_results[0].permalink)
@@ -381,7 +381,7 @@ Common issues to watch for:
     - **Create deliberate relations**: Connect each note to at least 2-3 related entities
     - **Use existing entities**: Before creating a new relation, search for existing entities
     - **Verify wikilinks**: When referencing `[[Entity]]`, use exact titles of existing notes
-    - **Check accuracy**: Use `search_notes()` or `recent_activity()` to confirm entity titles
+    - **Check accuracy**: Use `search()` or `recent_activity()` to confirm entity titles
     - **Use precise relation types**: Choose specific relation types that convey meaning (e.g., "implements" instead
       of "relates_to")
     - **Consider bidirectional relations**: When appropriate, create inverse relations in both entities

tests/api/test_knowledge_router.py

@@ -251,7 +251,7 @@ async def test_entity_indexing(client: AsyncClient):
 
     # Verify it's searchable
     search_response = await client.post(
-        "/search/", json={"text": "search", "entity_types": [SearchItemType.ENTITY.value]}
+        "/search/", json={"text": "search", "types": [SearchItemType.ENTITY.value]}
     )
     assert search_response.status_code == 200
     search_result = SearchResponse.model_validate(search_response.json())
@@ -279,7 +279,7 @@ async def test_entity_delete_indexing(client: AsyncClient):
 
     # Verify it's initially searchable
     search_response = await client.post(
-        "/search/", json={"text": "delete", "entity_types": [SearchItemType.ENTITY.value]}
+        "/search/", json={"text": "delete", "types": [SearchItemType.ENTITY.value]}
     )
     search_result = SearchResponse.model_validate(search_response.json())
     assert len(search_result.results) == 1
@@ -475,7 +475,7 @@ async def test_update_entity_search_index(client: AsyncClient):
 
     # Search should find new content
     search_response = await client.post(
-        "/search/", json={"text": "sphinx marker", "entity_types": [SearchItemType.ENTITY.value]}
+        "/search/", json={"text": "sphinx marker", "types": [SearchItemType.ENTITY.value]}
     )
     results = search_response.json()["results"]
     assert len(results) == 1

tests/api/test_resource_router.py

@@ -2,9 +2,9 @@
 
 import json
 from datetime import datetime, timezone
-from pathlib import Path
 
 import pytest
+from pathlib import Path
 
 from basic_memory.schemas import EntityResponse
 
@@ -346,7 +346,7 @@ async def test_put_resource_new_file(client, test_config, entity_repository, sea
     assert full_path.exists()
 
     # Verify file content
-    file_content = full_path.read_text(encoding="utf-8")
+    file_content = full_path.read_text()
     assert json.loads(file_content) == canvas_data
 
     # Verify entity was created in DB
@@ -420,7 +420,7 @@ async def test_put_resource_update_existing(client, test_config, entity_reposito
     assert response.status_code == 200
 
     # Verify file was updated
-    updated_content = full_path.read_text(encoding="utf-8")
+    updated_content = full_path.read_text()
     assert json.loads(updated_content) == updated_data
 
     # Verify entity was updated

tests/api/test_search_router.py

@@ -48,11 +48,11 @@ async def test_search_basic_pagination(client, indexed_entity):
 
 
 @pytest.mark.asyncio
-async def test_search_with_entity_type_filter(client, indexed_entity):
+async def test_search_with_type_filter(client, indexed_entity):
     """Test search with type filter."""
     # Should find with correct type
     response = await client.post(
-        "/search/", json={"text": "test", "entity_types": [SearchItemType.ENTITY.value]}
+        "/search/", json={"text": "test", "types": [SearchItemType.ENTITY.value]}
     )
     assert response.status_code == 200
     search_results = SearchResponse.model_validate(response.json())
@@ -60,7 +60,7 @@ async def test_search_with_entity_type_filter(client, indexed_entity):
 
     # Should find with relation type
     response = await client.post(
-        "/search/", json={"text": "test", "entity_types": [SearchItemType.RELATION.value]}
+        "/search/", json={"text": "test", "types": [SearchItemType.RELATION.value]}
     )
     assert response.status_code == 200
     search_results = SearchResponse.model_validate(response.json())
@@ -68,16 +68,16 @@ async def test_search_with_entity_type_filter(client, indexed_entity):
 
 
 @pytest.mark.asyncio
-async def test_search_with_type_filter(client, indexed_entity):
+async def test_search_with_entity_type_filter(client, indexed_entity):
     """Test search with entity type filter."""
     # Should find with correct entity type
-    response = await client.post("/search/", json={"text": "test", "types": ["test"]})
+    response = await client.post("/search/", json={"text": "test", "entity_types": ["test"]})
     assert response.status_code == 200
     search_results = SearchResponse.model_validate(response.json())
     assert len(search_results.results) == 1
 
     # Should not find with wrong entity type
-    response = await client.post("/search/", json={"text": "test", "types": ["note"]})
+    response = await client.post("/search/", json={"text": "test", "entity_types": ["note"]})
     assert response.status_code == 200
     search_results = SearchResponse.model_validate(response.json())
     assert len(search_results.results) == 0
@@ -153,8 +153,8 @@ async def test_multiple_filters(client, indexed_entity):
         "/search/",
         json={
             "text": "test",
-            "entity_types": [SearchItemType.ENTITY.value],
-            "types": ["test"],
+            "types": [SearchItemType.ENTITY.value],
+            "entity_types": ["test"],
             "after_date": datetime(2020, 1, 1, tzinfo=timezone.utc).isoformat(),
         },
     )

tests/cli/test_cli_tools.py

@@ -3,8 +3,6 @@
 These tests use real MCP tools with the test environment instead of mocks.
 """
 
-# Import for testing
-
 import io
 from datetime import datetime, timedelta
 import json
@@ -213,7 +211,7 @@ def test_search_basic(cli_env, setup_test_note):
     """Test basic search command."""
     result = runner.invoke(
         tool_app,
-        ["search-notes", "test observation"],
+        ["search", "test observation"],
     )
     assert result.exit_code == 0
 
@@ -237,7 +235,7 @@ def test_search_permalink(cli_env, setup_test_note):
 
     result = runner.invoke(
         tool_app,
-        ["search-notes", permalink, "--permalink"],
+        ["search", permalink, "--permalink"],
     )
     assert result.exit_code == 0
 
@@ -412,29 +410,3 @@ def test_continue_conversation_no_results(cli_env):
     # Check result contains expected content for no results
     assert "Continuing conversation on: NonexistentTopic" in result.stdout
     assert "The supplied query did not return any information" in result.stdout
-
-
-@patch("basic_memory.services.initialization.initialize_database")
-def test_ensure_migrations_functionality(mock_initialize_database, test_config, monkeypatch):
-    """Test the database initialization functionality."""
-    from basic_memory.services.initialization import ensure_initialization
-
-    # Call the function
-    ensure_initialization(test_config)
-
-    # The underlying asyncio.run should call our mocked function
-    mock_initialize_database.assert_called_once()
-
-
-@patch("basic_memory.services.initialization.initialize_database")
-def test_ensure_migrations_handles_errors(mock_initialize_database, test_config, monkeypatch):
-    """Test that initialization handles errors gracefully."""
-    from basic_memory.services.initialization import ensure_initialization
-
-    # Configure mock to raise an exception
-    mock_initialize_database.side_effect = Exception("Test error")
-
-    # Call the function - should not raise exception
-    ensure_initialization(test_config)
-
-    # We're just making sure it doesn't crash by calling it

tests/cli/test_import_chatgpt.py

@@ -1,11 +1,10 @@
 """Tests for import_chatgpt command."""
 
 import json
-
 import pytest
 from typer.testing import CliRunner
 
-from basic_memory.cli.app import app, import_app
+from basic_memory.cli.app import import_app, app
 from basic_memory.cli.commands import import_chatgpt
 from basic_memory.config import config
 from basic_memory.markdown import EntityParser, MarkdownProcessor
@@ -145,7 +144,7 @@ def sample_conversation_with_hidden():
 def sample_chatgpt_json(tmp_path, sample_conversation):
     """Create a sample ChatGPT JSON file."""
     json_file = tmp_path / "conversations.json"
-    with open(json_file, "w", encoding="utf-8") as f:
+    with open(json_file, "w") as f:
         json.dump([sample_conversation], f)
     return json_file
 
@@ -168,7 +167,7 @@ async def test_process_chatgpt_json(tmp_path, sample_chatgpt_json):
     assert conv_path.exists()
 
     # Check content formatting
-    content = conv_path.read_text(encoding="utf-8")
+    content = conv_path.read_text()
     assert "# Test Conversation" in content
     assert "### User" in content
     assert "Hello, this is a test message" in content
@@ -184,14 +183,14 @@ async def test_process_code_blocks(tmp_path, sample_conversation_with_code):
 
     # Create test file
     json_file = tmp_path / "code_test.json"
-    with open(json_file, "w", encoding="utf-8") as f:
+    with open(json_file, "w") as f:
         json.dump([sample_conversation_with_code], f)
 
     await import_chatgpt.process_chatgpt_json(json_file, tmp_path, processor)
 
     # Check content
     conv_path = tmp_path / "20250111-code-test.md"
-    content = conv_path.read_text(encoding="utf-8")
+    content = conv_path.read_text()
     assert "```python" in content
     assert "def hello():" in content
     assert "```" in content
@@ -205,7 +204,7 @@ async def test_hidden_messages(tmp_path, sample_conversation_with_hidden):
 
     # Create test file
     json_file = tmp_path / "hidden_test.json"
-    with open(json_file, "w", encoding="utf-8") as f:
+    with open(json_file, "w") as f:
         json.dump([sample_conversation_with_hidden], f)
 
     results = await import_chatgpt.process_chatgpt_json(json_file, tmp_path, processor)
@@ -215,7 +214,7 @@ async def test_hidden_messages(tmp_path, sample_conversation_with_hidden):
 
     # Check content
     conv_path = tmp_path / "20250111-hidden-test.md"
-    content = conv_path.read_text(encoding="utf-8")
+    content = conv_path.read_text()
     assert "Visible message" in content
     assert "Hidden message" not in content
 

tests/cli/test_import_claude_conversations.py

@@ -1,7 +1,6 @@
 """Tests for import_claude command (chat conversations)."""
 
 import json
-
 import pytest
 from typer.testing import CliRunner
 
@@ -45,7 +44,7 @@ def sample_conversation():
 def sample_conversations_json(tmp_path, sample_conversation):
     """Create a sample conversations.json file."""
     json_file = tmp_path / "conversations.json"
-    with open(json_file, "w", encoding="utf-8") as f:
+    with open(json_file, "w") as f:
         json.dump([sample_conversation], f)
     return json_file
 
@@ -66,7 +65,7 @@ async def test_process_chat_json(tmp_path, sample_conversations_json):
     # Check conversation file
     conv_path = tmp_path / "20250105-test-conversation.md"
     assert conv_path.exists()
-    content = conv_path.read_text(encoding="utf-8")
+    content = conv_path.read_text()
 
     # Check content formatting
     assert "### Human" in content
@@ -157,7 +156,7 @@ def test_import_conversation_with_attachments(tmp_path):
     }
 
     json_file = tmp_path / "with_attachments.json"
-    with open(json_file, "w", encoding="utf-8") as f:
+    with open(json_file, "w") as f:
         json.dump([conversation], f)
 
     # Set up environment
@@ -169,7 +168,7 @@ def test_import_conversation_with_attachments(tmp_path):
 
     # Check attachment formatting
     conv_path = tmp_path / "conversations/20250105-test-with-attachments.md"
-    content = conv_path.read_text(encoding="utf-8")
+    content = conv_path.read_text()
     assert "**Attachment: test.txt**" in content
     assert "```" in content
     assert "Test file content" in content

tests/cli/test_import_claude_projects.py

@@ -1,7 +1,6 @@
 """Tests for import_claude_projects command."""
 
 import json
-
 import pytest
 from typer.testing import CliRunner
 
@@ -44,7 +43,7 @@ def sample_project():
 def sample_projects_json(tmp_path, sample_project):
     """Create a sample projects.json file."""
     json_file = tmp_path / "projects.json"
-    with open(json_file, "w", encoding="utf-8") as f:
+    with open(json_file, "w") as f:
         json.dump([sample_project], f)
     return json_file
 
@@ -71,14 +70,14 @@ async def test_process_projects_json(tmp_path, sample_projects_json):
     # Check document files
     doc1 = project_dir / "docs/test-document.md"
     assert doc1.exists()
-    content1 = doc1.read_text(encoding="utf-8")
+    content1 = doc1.read_text()
     assert "# Test Document" in content1
     assert "This is test content" in content1
 
     # Check prompt template
     prompt = project_dir / "prompt-template.md"
     assert prompt.exists()
-    prompt_content = prompt.read_text(encoding="utf-8")
+    prompt_content = prompt.read_text()
     assert "# Test Prompt" in prompt_content
     assert "This is a test prompt" in prompt_content
 
@@ -161,7 +160,7 @@ def test_import_project_without_prompt(tmp_path):
     }
 
     json_file = tmp_path / "no_prompt.json"
-    with open(json_file, "w", encoding="utf-8") as f:
+    with open(json_file, "w") as f:
         json.dump([project], f)
 
     # Set up environment

tests/cli/test_import_memory_json.py

@@ -1,7 +1,6 @@
 """Tests for import_memory_json command."""
 
 import json
-
 import pytest
 from typer.testing import CliRunner
 
@@ -36,7 +35,7 @@ def sample_entities():
 def sample_json_file(tmp_path, sample_entities):
     """Create a sample memory.json file."""
     json_file = tmp_path / "memory.json"
-    with open(json_file, "w", encoding="utf-8") as f:
+    with open(json_file, "w") as f:
         for entity in sample_entities:
             f.write(json.dumps(entity) + "\n")
     return json_file
@@ -56,7 +55,7 @@ async def test_process_memory_json(tmp_path, sample_json_file):
     # Check file was created
     entity_file = tmp_path / "test/test_entity.md"
     assert entity_file.exists()
-    content = entity_file.read_text(encoding="utf-8")
+    content = entity_file.read_text()
     assert "Test observation 1" in content
     assert "Test observation 2" in content
     assert "test_relation [[related_entity]]" in content
@@ -121,7 +120,7 @@ def test_import_json_command_handle_old_format(tmp_path):
     ]
 
     json_file = tmp_path / "old_format.json"
-    with open(json_file, "w", encoding="utf-8") as f:
+    with open(json_file, "w") as f:
         for item in old_format:
             f.write(json.dumps(item) + "\n")
 

tests/cli/test_project_commands.py

@@ -15,13 +15,6 @@ from basic_memory.config import ConfigManager, DATA_DIR_NAME, CONFIG_FILE_NAME
 @pytest.fixture
 def temp_home(monkeypatch):
     """Create a temporary directory for testing."""
-    # Save the original environment variable if it exists
-    original_env = os.environ.get("BASIC_MEMORY_PROJECT")
-
-    # Clear environment variable for clean test
-    if "BASIC_MEMORY_PROJECT" in os.environ:
-        del os.environ["BASIC_MEMORY_PROJECT"]
-
     with TemporaryDirectory() as tempdir:
         temp_home = Path(tempdir)
         monkeypatch.setattr(Path, "home", lambda: temp_home)
@@ -32,12 +25,6 @@ def temp_home(monkeypatch):
 
         yield temp_home
 
-        # Cleanup: restore original environment variable if it existed
-        if original_env is not None:
-            os.environ["BASIC_MEMORY_PROJECT"] = original_env
-        elif "BASIC_MEMORY_PROJECT" in os.environ:
-            del os.environ["BASIC_MEMORY_PROJECT"]
-
 
 @pytest.fixture
 def cli_runner():
@@ -136,33 +123,17 @@ def test_project_default(cli_runner, temp_home):
     # Set as default
     result = cli_runner.invoke(app, ["project", "default", "test"])
     assert result.exit_code == 0
-    assert "Project 'test' set as default and activated" in result.stdout
+    assert "Project 'test' set as default" in result.stdout
 
     # Verify default was set
     config_manager = ConfigManager()
     assert config_manager.default_project == "test"
 
-    # Extra verification: check if the environment variable was set
-    assert os.environ.get("BASIC_MEMORY_PROJECT") == "test"
-
 
 def test_project_current(cli_runner, temp_home):
     """Test showing the current project."""
-    # Create a bare-bones config.json with main as the default project
-    config_file = temp_home / DATA_DIR_NAME / CONFIG_FILE_NAME
-    config_data = {
-        "projects": {
-            "main": str(temp_home / "basic-memory"),
-        },
-        "default_project": "main",
-    }
-    config_file.write_text(json.dumps(config_data))
 
-    # Create the main project directory
-    main_dir = temp_home / "basic-memory"
-    main_dir.mkdir(parents=True, exist_ok=True)
-
-    # Now check the current project
+    # Set as default
     result = cli_runner.invoke(app, ["project", "current"])
     assert result.exit_code == 0
     assert "Current project: main" in result.stdout
@@ -185,24 +156,3 @@ def test_project_option(cli_runner, temp_home, monkeypatch):
 
     # Verify environment variable was set
     assert env_vars.get("BASIC_MEMORY_PROJECT") == "test"
-
-
-def test_project_default_activates_project(cli_runner, temp_home, monkeypatch):
-    """Test that setting the default project also activates it in the current session."""
-    # Create a test environment
-    env = {}
-    monkeypatch.setattr(os, "environ", env)
-
-    # Create two test projects
-    config_manager = ConfigManager()
-    config_manager.add_project("project1", str(temp_home / "project1"))
-
-    # Set project1 as default using the CLI command
-    result = cli_runner.invoke(app, ["project", "default", "project1"])
-    assert result.exit_code == 0
-    assert "Project 'project1' set as default and activated" in result.stdout
-
-    # Verify the environment variable was set
-    # This is the core of our fix - the set_default_project command now also sets
-    # the BASIC_MEMORY_PROJECT environment variable to activate the project
-    assert env.get("BASIC_MEMORY_PROJECT") == "project1"

tests/cli/test_project_info.py

@@ -12,7 +12,7 @@ def test_info_stats_command(cli_env, test_graph):
     runner = CliRunner()
 
     # Run the command
-    result = runner.invoke(cli_app, ["project", "info"])
+    result = runner.invoke(cli_app, ["info", "stats"])
 
     # Verify exit code
     assert result.exit_code == 0
@@ -26,7 +26,7 @@ def test_info_stats_json(cli_env, test_graph):
     runner = CliRunner()
 
     # Run the command with --json flag
-    result = runner.invoke(cli_app, ["project", "info", "--json"])
+    result = runner.invoke(cli_app, ["info", "stats", "--json"])
 
     # Verify exit code
     assert result.exit_code == 0

tests/conftest.py

@@ -1,14 +1,14 @@
 """Common test fixtures."""
 
-from datetime import datetime, timezone
 from pathlib import Path
 from textwrap import dedent
 from typing import AsyncGenerator
+from datetime import datetime, timezone
 
 import pytest
 import pytest_asyncio
 from loguru import logger
-from sqlalchemy.ext.asyncio import AsyncEngine, AsyncSession, async_sessionmaker
+from sqlalchemy.ext.asyncio import AsyncSession, AsyncEngine, async_sessionmaker
 
 from basic_memory import db
 from basic_memory.config import ProjectConfig
@@ -140,7 +140,6 @@ def entity_parser(test_config):
 
 @pytest_asyncio.fixture
 async def sync_service(
-    test_config: ProjectConfig,
     entity_service: EntityService,
     entity_parser: EntityParser,
     entity_repository: EntityRepository,
@@ -150,7 +149,6 @@ async def sync_service(
 ) -> SyncService:
     """Create sync service for testing."""
     return SyncService(
-        config=test_config,
         entity_service=entity_service,
         entity_repository=entity_repository,
         relation_repository=relation_repository,
@@ -351,5 +349,5 @@ def test_files(test_config) -> dict[str, Path]:
 @pytest_asyncio.fixture
 async def synced_files(sync_service, test_config, test_files):
     # Initial sync - should create forward reference
-    await sync_service.sync(test_config.home)
+    await sync_service.sync(test_config.home, show_progress=False)
     return test_files

tests/markdown/test_entity_parser.py

@@ -217,37 +217,6 @@ def test_parse_empty_content():
     assert len(result.relations) == 0
 
 
-@pytest.mark.asyncio
-async def test_parse_file_with_absolute_path(test_config, entity_parser):
-    """Test parsing a file with an absolute path."""
-    content = dedent("""
-        ---
-        type: component
-        permalink: absolute_path_test
-        ---
-
-        # Absolute Path Test
-        
-        A file with an absolute path.
-        """)
-
-    # Create a test file in the project directory
-    test_file = test_config.home / "absolute_path_test.md"
-    test_file.write_text(content)
-
-    # Get the absolute path to the test file
-    absolute_path = test_file.resolve()
-
-    # Parse the file using the absolute path
-    entity = await entity_parser.parse_file(absolute_path)
-
-    # Verify the file was parsed correctly
-    assert entity.frontmatter.permalink == "absolute_path_test"
-    assert "Absolute Path Test" in entity.content
-    assert entity.created is not None
-    assert entity.modified is not None
-
-
 # @pytest.mark.asyncio
 # async def test_parse_file_invalid_yaml(test_config, entity_parser):
 #     """Test parsing file with invalid YAML frontmatter."""

tests/markdown/test_markdown_processor.py

@@ -8,10 +8,10 @@ from pathlib import Path
 
 import pytest
 
-from basic_memory.markdown.markdown_processor import DirtyFileError, MarkdownProcessor
+from basic_memory.markdown.markdown_processor import MarkdownProcessor, DirtyFileError
 from basic_memory.markdown.schemas import (
-    EntityFrontmatter,
     EntityMarkdown,
+    EntityFrontmatter,
     Observation,
     Relation,
 )
@@ -41,7 +41,7 @@ async def test_write_new_minimal_file(markdown_processor: MarkdownProcessor, tmp
     await markdown_processor.write_file(path, markdown)
 
     # Read back and verify
-    content = path.read_text(encoding="utf-8")
+    content = path.read_text()
     assert "---" in content  # Has frontmatter
     assert "type: note" in content
     assert "permalink: test" in content
@@ -90,7 +90,7 @@ async def test_write_new_file_with_content(markdown_processor: MarkdownProcessor
     await markdown_processor.write_file(path, markdown)
 
     # Read back and verify
-    content = path.read_text(encoding="utf-8")
+    content = path.read_text()
 
     # Check content preserved exactly
     assert "# Custom Title" in content
@@ -169,7 +169,7 @@ async def test_dirty_file_detection(markdown_processor: MarkdownProcessor, tmp_p
     checksum = await markdown_processor.write_file(path, initial)
 
     # Modify file directly
-    path.write_text(path.read_text(encoding="utf-8") + "\nModified!")
+    path.write_text(path.read_text() + "\nModified!")
 
     # Try to update with old checksum
     update = EntityMarkdown(

tests/mcp/test_tool_canvas.py

@@ -46,7 +46,7 @@ async def test_create_canvas(app, test_config):
     assert file_path.exists()
 
     # Verify content is correct
-    content = json.loads(file_path.read_text(encoding="utf-8"))
+    content = json.loads(file_path.read_text())
     assert content["nodes"] == nodes
     assert content["edges"] == edges
 
@@ -81,7 +81,7 @@ async def test_create_canvas_with_extension(app, test_config):
     assert file_path.exists()
 
     # Verify content
-    content = json.loads(file_path.read_text(encoding="utf-8"))
+    content = json.loads(file_path.read_text())
     assert content["nodes"] == nodes
 
 
@@ -134,7 +134,7 @@ async def test_update_existing_canvas(app, test_config):
     assert "Updated: visualizations/update-test.canvas" in result
 
     # Verify content was updated
-    content = json.loads(file_path.read_text(encoding="utf-8"))
+    content = json.loads(file_path.read_text())
     assert content["nodes"] == updated_nodes
     assert content["edges"] == updated_edges
 
@@ -252,7 +252,7 @@ async def test_create_canvas_complex_content(app, test_config):
     assert file_path.exists()
 
     # Verify content is correct with all complex structures
-    content = json.loads(file_path.read_text(encoding="utf-8"))
+    content = json.loads(file_path.read_text())
     assert len(content["nodes"]) == 4
     assert len(content["edges"]) == 2
 

tests/mcp/test_tool_memory.py

@@ -5,9 +5,12 @@ from datetime import datetime
 
 from mcp.server.fastmcp.exceptions import ToolError
 
-from basic_memory.mcp.tools import build_context
+from basic_memory.mcp.tools import build_context, recent_activity
 from basic_memory.schemas.memory import (
     GraphContext,
+    EntitySummary,
+    ObservationSummary,
+    RelationSummary,
 )
 
 
@@ -80,6 +83,53 @@ invalid_timeframes = [
 ]
 
 
+@pytest.mark.asyncio
+async def test_recent_activity_timeframe_formats(client, test_graph):
+    """Test that recent_activity accepts various timeframe formats."""
+    # Test each valid timeframe
+    for timeframe in valid_timeframes:
+        try:
+            result = await recent_activity(
+                type=["entity"], timeframe=timeframe, page=1, page_size=10, max_related=10
+            )
+            assert result is not None
+        except Exception as e:
+            pytest.fail(f"Failed with valid timeframe '{timeframe}': {str(e)}")
+
+    # Test invalid timeframes should raise ValidationError
+    for timeframe in invalid_timeframes:
+        with pytest.raises(ToolError):
+            await recent_activity(timeframe=timeframe)
+
+
+@pytest.mark.asyncio
+async def test_recent_activity_type_filters(client, test_graph):
+    """Test that recent_activity correctly filters by types."""
+    # Test single type
+    result = await recent_activity(type=["entity"])
+    assert result is not None
+    assert all(isinstance(r, EntitySummary) for r in result.primary_results)
+
+    # Test multiple types
+    result = await recent_activity(type=["entity", "observation"])
+    assert result is not None
+    assert all(
+        isinstance(r, EntitySummary) or isinstance(r, ObservationSummary)
+        for r in result.primary_results
+    )
+
+    # Test all types
+    result = await recent_activity(type=["entity", "observation", "relation"])
+    assert result is not None
+    # Results can be any type
+    assert all(
+        isinstance(r, EntitySummary)
+        or isinstance(r, ObservationSummary)
+        or isinstance(r, RelationSummary)
+        for r in result.primary_results
+    )
+
+
 @pytest.mark.asyncio
 async def test_build_context_timeframe_formats(client, test_graph):
     """Test that build_context accepts various timeframe formats."""

tests/mcp/test_tool_notes.py

@@ -1,6 +1,7 @@
 """Tests for note tools that exercise the full stack with SQLite."""
 
 from textwrap import dedent
+
 import pytest
 
 from basic_memory.mcp.tools import write_note, read_note, delete_note
@@ -26,10 +27,8 @@ async def test_write_note(app):
     assert result
     assert (
         dedent("""
-        # Created note
-        file_path: test/Test Note.md
+        # Created test/Test Note.md (159f2168)
         permalink: test/test-note
-        checksum: 159f2168
         
         ## Tags
         - test, documentation
@@ -65,10 +64,8 @@ async def test_write_note_no_tags(app):
     assert result
     assert (
         dedent("""
-        # Created note
-        file_path: test/Simple Note.md
+        # Created test/Simple Note.md (9a1ff079)
         permalink: test/simple-note
-        checksum: 9a1ff079
         """).strip()
         in result
     )
@@ -108,10 +105,8 @@ async def test_write_note_update_existing(app):
     assert result  # Got a valid permalink
     assert (
         dedent("""
-        # Created note
-        file_path: test/Test Note.md
+        # Created test/Test Note.md (159f2168)
         permalink: test/test-note
-        checksum: 159f2168
         
         ## Tags
         - test, documentation
@@ -127,10 +122,8 @@ async def test_write_note_update_existing(app):
     )
     assert (
         dedent("""
-        # Updated note
-        file_path: test/Test Note.md
+        # Updated test/Test Note.md (a8eb4d44)
         permalink: test/test-note
-        checksum: a8eb4d44
         
         ## Tags
         - test, documentation
@@ -194,30 +187,6 @@ async def test_delete_note_doesnt_exist(app):
     assert deleted is False
 
 
-@pytest.mark.asyncio
-async def test_write_note_with_tag_array_from_bug_report(app):
-    """Test creating a note with a tag array as reported in issue #38.
-
-    This reproduces the exact payload from the bug report where Cursor
-    was passing an array of tags and getting a type mismatch error.
-    """
-    # This is the exact payload from the bug report
-    bug_payload = {
-        "title": "Title",
-        "folder": "folder",
-        "content": "CONTENT",
-        "tags": ["hipporag", "search", "fallback", "symfony", "error-handling"],
-    }
-
-    # Try to call the function with this data directly
-    result = await write_note(**bug_payload)
-
-    assert result
-    assert "permalink: folder/title" in result
-    assert "Tags" in result
-    assert "hipporag" in result
-
-
 @pytest.mark.asyncio
 async def test_write_note_verbose(app):
     """Test creating a new note.
@@ -243,10 +212,8 @@ async def test_write_note_verbose(app):
 
     assert (
         dedent("""
-        # Created note
-        file_path: test/Test Note.md
+        # Created test/Test Note.md (06873a7a)
         permalink: test/test-note
-        checksum: 06873a7a
         
         ## Observations
         - note: 1
@@ -262,118 +229,3 @@ async def test_write_note_verbose(app):
         """).strip()
         in result
     )
-
-
-@pytest.mark.asyncio
-async def test_write_note_preserves_custom_metadata(app, test_config):
-    """Test that updating a note preserves custom metadata fields.
-
-    Reproduces issue #36 where custom frontmatter fields like Status
-    were being lost when updating notes with the write_note tool.
-
-    Should:
-    - Create a note with custom frontmatter
-    - Update the note with new content
-    - Verify custom frontmatter is preserved
-    """
-    # First, create a note with custom metadata using write_note
-    await write_note(
-        title="Custom Metadata Note",
-        folder="test",
-        content="# Initial content",
-        tags=["test"],
-    )
-
-    # Read the note to get its permalink
-    content = await read_note("test/custom-metadata-note")
-
-    # Now directly update the file with custom frontmatter
-    # We need to use a direct file update to add custom frontmatter
-    import frontmatter
-
-    file_path = test_config.home / "test" / "Custom Metadata Note.md"
-    post = frontmatter.load(file_path)
-
-    # Add custom frontmatter
-    post["Status"] = "In Progress"
-    post["Priority"] = "High"
-    post["Version"] = "1.0"
-
-    # Write the file back
-    with open(file_path, "w") as f:
-        f.write(frontmatter.dumps(post))
-
-    # Now update the note using write_note
-    result = await write_note(
-        title="Custom Metadata Note",
-        folder="test",
-        content="# Updated content",
-        tags=["test", "updated"],
-    )
-
-    # Verify the update was successful
-    assert ("Updated note\nfile_path: test/Custom Metadata Note.md") in result
-
-    # Read the note back and check if custom frontmatter is preserved
-    content = await read_note("test/custom-metadata-note")
-
-    # Custom frontmatter should be preserved
-    assert "Status: In Progress" in content
-    assert "Priority: High" in content
-    # Version might be quoted as '1.0' due to YAML serialization
-    assert "Version:" in content  # Just check that the field exists
-    assert "1.0" in content  # And that the value exists somewhere
-
-    # And new content should be there
-    assert "# Updated content" in content
-
-    # And tags should be updated
-    assert "'#test'" in content
-    assert "'#updated'" in content
-
-
-@pytest.mark.asyncio
-async def test_write_note_preserves_content_frontmatter(app):
-    """Test creating a new note."""
-    await write_note(
-        title="Test Note",
-        folder="test",
-        content=dedent(
-            """
-            ---
-            title: Test Note
-            type: note
-            version: 1.0 
-            author: name
-            ---
-            # Test
-            
-            This is a test note
-            """
-        ),
-        tags=["test", "documentation"],
-    )
-
-    # Try reading it back via permalink
-    content = await read_note("test/test-note")
-    assert (
-        dedent(
-            """
-            ---
-            title: Test Note
-            type: note
-            permalink: test/test-note
-            version: 1.0
-            author: name
-            tags:
-            - '#test'
-            - '#documentation'
-            ---
-            
-            # Test
-            
-            This is a test note
-            """
-        ).strip()
-        in content
-    )

tests/mcp/test_tool_read_note.py

@@ -26,7 +26,7 @@ async def mock_call_get():
 @pytest_asyncio.fixture
 async def mock_search():
     """Mock for search tool."""
-    with patch("basic_memory.mcp.tools.read_note.search_notes") as mock:
+    with patch("basic_memory.mcp.tools.read_note.search") as mock:
         # Default to empty results
         mock.return_value = SearchResponse(results=[], current_page=1, page_size=1)
         yield mock
@@ -51,10 +51,8 @@ async def test_note_unicode_content(app):
 
     assert (
         dedent("""
-        # Created note
-        file_path: test/Unicode Test.md
+        # Created test/Unicode Test.md (272389cd)
         permalink: test/unicode-test
-        checksum: 272389cd
         """).strip()
         in result
     )
@@ -203,8 +201,7 @@ async def test_read_note_title_search_fallback(mock_call_get, mock_search):
 
     # Verify title search was used
     mock_search.assert_called_once()
-    assert mock_search.call_args[1]["query"] == "Test Note"
-    assert mock_search.call_args[1]["search_type"] == "title"
+    assert mock_search.call_args[0][0].title == "Test Note"
 
     # Verify second lookup was used
     assert mock_call_get.call_count == 2
@@ -257,17 +254,15 @@ async def test_read_note_text_search_fallback(mock_call_get, mock_search):
 
     # Verify both search types were used
     assert mock_search.call_count == 2
-    assert mock_search.call_args_list[0][1]["query"] == "some query"  # Title search
-    assert mock_search.call_args_list[0][1]["search_type"] == "title"
-    assert mock_search.call_args_list[1][1]["query"] == "some query"  # Text search
-    assert mock_search.call_args_list[1][1]["search_type"] == "text"
+    assert mock_search.call_args_list[0][0][0].title == "some query"  # Title search
+    assert mock_search.call_args_list[1][0][0].text == "some query"  # Text search
 
     # Verify result contains helpful information
     assert "Note Not Found" in result
     assert "Related Note 1" in result
     assert "Related Note 2" in result
     assert 'read_note("notes/related-note-1")' in result
-    assert "search_notes(query=" in result
+    assert "search(query=" in result
     assert "write_note(" in result
 
 

tests/mcp/test_tool_recent_activity.py

@@ -1,110 +0,0 @@
-"""Tests for discussion context MCP tool."""
-
-import pytest
-
-from mcp.server.fastmcp.exceptions import ToolError
-
-from basic_memory.mcp.tools import recent_activity
-from basic_memory.schemas.memory import (
-    EntitySummary,
-    ObservationSummary,
-    RelationSummary,
-)
-from basic_memory.schemas.search import SearchItemType
-
-# Test data for different timeframe formats
-valid_timeframes = [
-    "7d",  # Standard format
-    "yesterday",  # Natural language
-    "0d",  # Zero duration
-]
-
-invalid_timeframes = [
-    "invalid",  # Nonsense string
-    "tomorrow",  # Future date
-]
-
-
-@pytest.mark.asyncio
-async def test_recent_activity_timeframe_formats(client, test_graph):
-    """Test that recent_activity accepts various timeframe formats."""
-    # Test each valid timeframe
-    for timeframe in valid_timeframes:
-        try:
-            result = await recent_activity(
-                type=["entity"], timeframe=timeframe, page=1, page_size=10, max_related=10
-            )
-            assert result is not None
-        except Exception as e:
-            pytest.fail(f"Failed with valid timeframe '{timeframe}': {str(e)}")
-
-    # Test invalid timeframes should raise ValidationError
-    for timeframe in invalid_timeframes:
-        with pytest.raises(ToolError):
-            await recent_activity(timeframe=timeframe)
-
-
-@pytest.mark.asyncio
-async def test_recent_activity_type_filters(client, test_graph):
-    """Test that recent_activity correctly filters by types."""
-
-    # Test single string type
-    result = await recent_activity(type=SearchItemType.ENTITY)
-    assert result is not None
-    assert all(isinstance(r, EntitySummary) for r in result.primary_results)
-
-    # Test single string type
-    result = await recent_activity(type="entity")
-    assert result is not None
-    assert all(isinstance(r, EntitySummary) for r in result.primary_results)
-
-    # Test single type
-    result = await recent_activity(type=["entity"])
-    assert result is not None
-    assert all(isinstance(r, EntitySummary) for r in result.primary_results)
-
-    # Test multiple types
-    result = await recent_activity(type=["entity", "observation"])
-    assert result is not None
-    assert all(
-        isinstance(r, EntitySummary) or isinstance(r, ObservationSummary)
-        for r in result.primary_results
-    )
-
-    # Test multiple types
-    result = await recent_activity(type=[SearchItemType.ENTITY, SearchItemType.OBSERVATION])
-    assert result is not None
-    assert all(
-        isinstance(r, EntitySummary) or isinstance(r, ObservationSummary)
-        for r in result.primary_results
-    )
-
-    # Test all types
-    result = await recent_activity(type=["entity", "observation", "relation"])
-    assert result is not None
-    # Results can be any type
-    assert all(
-        isinstance(r, EntitySummary)
-        or isinstance(r, ObservationSummary)
-        or isinstance(r, RelationSummary)
-        for r in result.primary_results
-    )
-
-
-@pytest.mark.asyncio
-async def test_recent_activity_type_invalid(client, test_graph):
-    """Test that recent_activity correctly filters by types."""
-
-    # Test single invalid string type
-    with pytest.raises(ValueError) as e:
-        await recent_activity(type="note")
-    assert (
-        str(e.value) == "Invalid type: note. Valid types are: ['entity', 'observation', 'relation']"
-    )
-
-    # Test invalid string array type
-    with pytest.raises(ValueError) as e:
-        await recent_activity(type=["note"])
-    assert (
-        str(e.value) == "Invalid type: note. Valid types are: ['entity', 'observation', 'relation']"
-    )

tests/mcp/test_tool_resource.py

@@ -42,33 +42,6 @@ async def test_read_file_text_file(app, synced_files):
     assert response["encoding"] == "utf-8"
 
 
-@pytest.mark.asyncio
-async def test_read_content_file_path(app, synced_files):
-    """Test reading a text file.
-
-    Should:
-    - Correctly identify text content
-    - Return the content as text
-    - Include correct metadata
-    """
-    # First create a text file via notes
-    result = await write_note(
-        title="Text Resource",
-        folder="test",
-        content="This is a test text resource",
-        tags=["test", "resource"],
-    )
-    assert result is not None
-
-    # Now read it as a resource
-    response = await read_content("test/Text Resource.md")
-
-    assert response["type"] == "text"
-    assert "This is a test text resource" in response["text"]
-    assert response["content_type"].startswith("text/")
-    assert response["encoding"] == "utf-8"
-
-
 @pytest.mark.asyncio
 async def test_read_file_image_file(app, synced_files):
     """Test reading an image file.

tests/mcp/test_tool_search.py

@@ -4,11 +4,12 @@ import pytest
 from datetime import datetime, timedelta
 
 from basic_memory.mcp.tools import write_note
-from basic_memory.mcp.tools.search import search_notes
+from basic_memory.mcp.tools.search import search
+from basic_memory.schemas.search import SearchQuery, SearchItemType
 
 
 @pytest.mark.asyncio
-async def test_search_text(client):
+async def test_search_basic(client):
     """Test basic search functionality."""
     # Create a test note
     result = await write_note(
@@ -20,67 +21,8 @@ async def test_search_text(client):
     assert result
 
     # Search for it
-    response = await search_notes(query="searchable")
-
-    # Verify results
-    assert len(response.results) > 0
-    assert any(r.permalink == "test/test-search-note" for r in response.results)
-
-
-@pytest.mark.asyncio
-async def test_search_title(client):
-    """Test basic search functionality."""
-    # Create a test note
-    result = await write_note(
-        title="Test Search Note",
-        folder="test",
-        content="# Test\nThis is a searchable test note",
-        tags=["test", "search"],
-    )
-    assert result
-
-    # Search for it
-    response = await search_notes(query="Search Note", search_type="title")
-
-    # Verify results
-    assert len(response.results) > 0
-    assert any(r.permalink == "test/test-search-note" for r in response.results)
-
-
-@pytest.mark.asyncio
-async def test_search_permalink(client):
-    """Test basic search functionality."""
-    # Create a test note
-    result = await write_note(
-        title="Test Search Note",
-        folder="test",
-        content="# Test\nThis is a searchable test note",
-        tags=["test", "search"],
-    )
-    assert result
-
-    # Search for it
-    response = await search_notes(query="test/test-search-note", search_type="permalink")
-
-    # Verify results
-    assert len(response.results) > 0
-    assert any(r.permalink == "test/test-search-note" for r in response.results)
-
-
-@pytest.mark.asyncio
-async def test_search_permalink_match(client):
-    """Test basic search functionality."""
-    # Create a test note
-    result = await write_note(
-        title="Test Search Note",
-        folder="test",
-        content="# Test\nThis is a searchable test note",
-        tags=["test", "search"],
-    )
-    assert result
-
-    # Search for it
-    response = await search_notes(query="test/test-search-*", search_type="permalink")
+    query = SearchQuery(text="searchable")
+    response = await search(query)
 
     # Verify results
     assert len(response.results) > 0
@@ -100,7 +42,8 @@ async def test_search_pagination(client):
     assert result
 
     # Search for it
-    response = await search_notes(query="searchable", page=1, page_size=1)
+    query = SearchQuery(text="searchable")
+    response = await search(query, page=1, page_size=1)
 
     # Verify results
     assert len(response.results) == 1
@@ -118,24 +61,8 @@ async def test_search_with_type_filter(client):
     )
 
     # Search with type filter
-    response = await search_notes(query="type", types=["note"])
-
-    # Verify all results are entities
-    assert all(r.type == "entity" for r in response.results)
-
-
-@pytest.mark.asyncio
-async def test_search_with_entity_type_filter(client):
-    """Test search with entity type filter."""
-    # Create test content
-    await write_note(
-        title="Entity Type Test",
-        folder="test",
-        content="# Test\nFiltered by type",
-    )
-
-    # Search with entity type filter
-    response = await search_notes(query="type", entity_types=["entity"])
+    query = SearchQuery(text="type", types=[SearchItemType.ENTITY])
+    response = await search(query)
 
     # Verify all results are entities
     assert all(r.type == "entity" for r in response.results)
@@ -153,7 +80,8 @@ async def test_search_with_date_filter(client):
 
     # Search with date filter
     one_hour_ago = datetime.now() - timedelta(hours=1)
-    response = await search_notes(query="recent", after_date=one_hour_ago.isoformat())
+    query = SearchQuery(text="recent", after_date=one_hour_ago)
+    response = await search(query)
 
     # Verify we get results within timeframe
     assert len(response.results) > 0

tests/schemas/test_search.py

@@ -32,12 +32,12 @@ def test_search_filters():
     """Test search result filtering."""
     query = SearchQuery(
         text="search",
-        entity_types=[SearchItemType.ENTITY],
-        types=["component"],
+        types=[SearchItemType.ENTITY],
+        entity_types=["component"],
         after_date=datetime(2024, 1, 1),
     )
-    assert query.entity_types == [SearchItemType.ENTITY]
-    assert query.types == ["component"]
+    assert query.types == [SearchItemType.ENTITY]
+    assert query.entity_types == ["component"]
     assert query.after_date == "2024-01-01T00:00:00"
 
 

tests/services/test_entity_service.py

@@ -6,14 +6,12 @@ from textwrap import dedent
 import pytest
 import yaml
 
-from basic_memory.config import ProjectConfig
-from basic_memory.markdown import EntityParser
 from basic_memory.models import Entity as EntityModel
 from basic_memory.repository import EntityRepository
 from basic_memory.schemas import Entity as EntitySchema
 from basic_memory.services import FileService
 from basic_memory.services.entity_service import EntityService
-from basic_memory.services.exceptions import EntityCreationError, EntityNotFoundError
+from basic_memory.services.exceptions import EntityNotFoundError, EntityCreationError
 from basic_memory.utils import generate_permalink
 
 
@@ -263,7 +261,7 @@ async def test_get_entities_by_permalinks(entity_service: EntityService):
 
 
 @pytest.mark.asyncio
-async def test_get_entities_empty_input(entity_service: EntityService):
+async def test_oget_entities_empty_input(entity_service: EntityService):
     """Test opening nodes with empty path ID list."""
     found = await entity_service.get_entities_by_permalinks([])
     assert len(found) == 0
@@ -523,7 +521,7 @@ async def test_update_with_content(entity_service: EntityService, file_service:
         """
     ).strip()
 
-    # update entity
+    # Create test entity
     entity, created = await entity_service.create_or_update_entity(
         EntitySchema(
             title="Git Workflow Guide",
@@ -559,33 +557,3 @@ async def test_update_with_content(entity_service: EntityService, file_service:
 
     # assert content is in file
     assert update_content.strip() == file_content
-
-
-@pytest.mark.asyncio
-async def test_create_with_no_frontmatter(
-    test_config: ProjectConfig,
-    entity_parser: EntityParser,
-    entity_service: EntityService,
-    file_service: FileService,
-):
-    # contains no frontmatter
-    content = "# Git Workflow Guide"
-    file_path = Path("test/Git Workflow Guide.md")
-    full_path = test_config.home / file_path
-
-    await file_service.write_file(Path(full_path), content)
-
-    entity_markdown = await entity_parser.parse_file(full_path)
-    created = await entity_service.create_entity_from_markdown(file_path, entity_markdown)
-    file_content, _ = await file_service.read_file(created.file_path)
-
-    assert str(file_path) == str(created.file_path)
-    assert created.title == "Git Workflow Guide"
-    assert created.entity_type == "note"
-    assert created.permalink is None
-
-    # assert file
-    expected = dedent("""
-        # Git Workflow Guide
-        """).strip()
-    assert expected == file_content