chore(release): 0.12.2 [skip ci]

fix: utf8 for all file reads/write/open instead of default platform encoding (#91 )
Signed-off-by: phernandez <paul@basicmachines.co>
2026-06-21 13:47:35 +00:00 · 2025-04-08 16:27:42 +00:00 · 2025-04-08 10:55:01 -05:00 · 2025-04-07 22:47:23 +00:00 · 2025-04-07 17:45:26 -05:00 · 2025-04-06 20:29:00 -05:00
90 changed files with 3306 additions and 1140 deletions
@@ -0,0 +1,16 @@
+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 }}
@@ -5,6 +5,12 @@ 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:
@@ -47,4 +47,8 @@ ENV/
 # obsidian docs:
 /docs/.obsidian/
 /examples/.obsidian/
-/examples/.basic-memory/
+/examples/.basic-memory/
+
+
+# claude action
+claude-output
@@ -1,6 +1,234 @@
 # CHANGELOG


+## 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
@@ -37,6 +37,7 @@ 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

@@ -63,7 +64,7 @@ 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 enviroment with in memory SQLite and tmp_file directory
+- Each test runs in a standalone environment with in memory SQLite and tmp_file directory

 ## BASIC MEMORY PRODUCT USAGE

@@ -106,7 +107,7 @@ See the [README.md](README.md) file for a project overview.
      1d", "1 week")

  **Search & Discovery:**
-    - `search(query, page, page_size)` - Full-text search across all content with filtering options
+    - `search_notes(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
@@ -114,7 +115,7 @@ 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(query, after_date)` - Search with detailed, formatted results for better context understanding
+    - `search_notes(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

@@ -134,30 +135,32 @@ could achieve independently.

 ## GitHub Integration

-Basic Memory has taken AI-Human collaboration to the next level by integrating Claude directly into the development workflow through GitHub:
+Basic Memory uses Claude directly into the development workflow through GitHub:

 ### GitHub MCP Tools

-Using the GitHub Model Context Protocol server, Claude can now:
+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
+    - 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
+    - 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
+    - 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.
+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

@@ -168,4 +171,5 @@ With GitHub integration, the development workflow includes:
 3. **Branch management** - Claude can create feature branches for implementations
 4. **Documentation maintenance** - Claude can keep documentation updated as the code evolves

-This level of integration represents a new paradigm in AI-human collaboration, where the AI assistant becomes a full-fledged team member rather than just a tool for generating code snippets.
+With this integration, the AI assistant is a full-fledged team member rather than just a tool for generating code
+snippets.
@@ -3,6 +3,8 @@
 [![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
@@ -11,8 +13,8 @@ Basic Memory lets you build persistent knowledge through natural conversations w
 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: http://basicmachines.co
- Documentation: http://memory.basicmachines.co
+- Website: https://basicmachines.co
+- Documentation: https://memory.basicmachines.co

 ## Pick up your conversation right where you left off

@@ -151,7 +153,7 @@ The note embeds semantic content and links to other topics via simple Markdown f

 3. You see this file on your computer in real time in the current project directory (default `~/$HOME/basic-memory`).

- Realtime sync can be enabled via running `basic-memory sync --watch`
+- Realtime sync is enabled by default with the v0.12.0 version

 4. In a chat with the LLM, you can reference a topic:

@@ -260,6 +262,43 @@ Examples of relations:
 - documented_in [[Coffee Journal]]
 ```

+## Using with VS Code
+For one-click installation, click one of the install buttons below...
+
+[![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)
+
+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.
+
+### Manual Installation
+
+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)`.
+
+```json
+{
+  "mcp": {
+    "servers": {
+      "basic-memory": {
+        "command": "uvx",
+        "args": ["basic-memory", "mcp"]
+      }
+    }
+  }
+}
+```
+
+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.
+
+```json
+{
+  "servers": {
+    "basic-memory": {
+      "command": "uvx",
+      "args": ["basic-memory", "mcp"]
+    }
+  }
+}
+```
+
 ## Using with Claude Desktop

 Basic Memory is built using the MCP (Model Context Protocol) and works with the Claude desktop app (https://claude.ai/):
@@ -283,7 +322,8 @@ for OS X):
 }
 ```

-If you want to use a specific project (see [Multiple Projects](#multiple-projects) below), update your Claude Desktop
+If you want to use a specific project (see [Multiple Projects](docs/User%20Guide.md#multiple-projects)), update your
+Claude Desktop
 config:

 ```json
@@ -304,13 +344,7 @@ config:

 2. Sync your knowledge:

-```bash
-# One-time sync of local knowledge updates
-basic-memory sync
-
-# Run realtime sync process (recommended)
-basic-memory sync --watch
-```
+Basic Memory will sync the files in your project in real time if you make manual edits.

 3. In Claude Desktop, the LLM can now use these tools:

@@ -318,7 +352,7 @@ basic-memory sync --watch
 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(query, page, page_size) - Search across your knowledge base
+search_notes(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
 ```
@@ -349,4 +383,14 @@ AGPL-3.0
 Contributions are welcome. See the [Contributing](CONTRIBUTING.md) guide for info about setting up the project locally
 and submitting PRs.

-Built with ♥️ by Basic Machines
+## 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
@@ -0,0 +1,13 @@
+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...
@@ -0,0 +1,35 @@
+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---
@@ -0,0 +1,49 @@
+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
@@ -4,6 +4,8 @@ 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).
@@ -51,7 +53,7 @@ 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(
+results = await search_notes(
    query="authentication system",      # Text to search for
    page=1,                             # Optional: Pagination
    page_size=10                        # Optional: Results per page
@@ -152,7 +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() to find relevant notes]
+   [Use search_notes() to find relevant notes]
   [Then build_context() to understand connections]
   ```

@@ -249,7 +251,7 @@ 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("travel")
+    search_results = await search_notes("travel")
    existing_entities = [result.title for result in search_results.primary_results]
    
    # Check if specific entities exist
@@ -321,7 +323,7 @@ Common issues to watch for:
       content = await read_note("Document")
   except:
       # Try search instead
-       results = await search("Document")
+       results = await search_notes("Document")
       if results and results.primary_results:
           # Found something similar
           content = await read_note(results.primary_results[0].permalink)
@@ -367,7 +369,7 @@ 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()` or `recent_activity()` to confirm entity titles
+   - **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

@@ -21,15 +21,30 @@ basic-memory sync
 # Watch for changes
 basic-memory sync --watch

-# Sync specific folder
-basic-memory sync path/to/folder
+# Show detailed sync information
+basic-memory sync --verbose
 ```

 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:
@@ -43,13 +58,13 @@ basic-memory import claude projects

 # ChatGPT history
 basic-memory import chatgpt
+
+# ChatGPT history
+basic-memory import memory-json /path/to/memory.json
+
 ```

-Options:
- `--folder PATH`: Target folder for imported content
- `--overwrite`: Replace existing files
- `--skip-existing`: Keep existing files
-
+> **Note**: After importing, run `basic-memory sync` to index the new files.
 ### status

 Shows system status information:
@@ -242,10 +257,12 @@ 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:

 ```
@@ -258,6 +275,32 @@ 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

@@ -14,6 +14,10 @@ It can be used with any service that supports the MCP, but Claude Desktop works

 ## 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
@@ -26,14 +30,32 @@ 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.
+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

-Claude Desktop often has trouble finding executables in your user path. Follow these steps for a reliable setup:
+Edit your Claude Desktop config, located at `~/Library/Application Support/Claude/claude_desktop_config.json`:

-#### Step 1: Find the absolute path to uvx
+```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**

 Open Terminal and run:

@@ -43,9 +65,9 @@ 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 configuration file located at `~/Library/Application Support/Claude/claude_desktop_config.json`:
+Edit the Claude Desktop config:

 ```json
 {
@@ -63,26 +85,15 @@ Edit the configuration file located at `~/Library/Application Support/Claude/cla

 Replace `/absolute/path/to/uvx` with the actual path you found in Step 1.

-> **Note**: Using absolute paths is necessary because Claude Desktop cannot access binaries in your user PATH.
-
-#### Step 3: Restart Claude Desktop
+**Step 3: Restart Claude Desktop**

 Close and reopen Claude Desktop for the changes to take effect.

-### 3. Start the Sync Service
+### 3. Sync changes in real time

-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.
+> **Note**: The service will sync changes from your project directory in real time so they available for the AI assistant. 

+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:
@@ -97,6 +108,21 @@ 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
@@ -108,8 +134,8 @@ 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**: Ensure `basic-memory sync --watch` is running
-
+4. **Check sync status**: You can view the sync status by running `basic-memory status
+.
 #### Permission Issues

 If you encounter permission errors:
@@ -119,30 +145,24 @@ If you encounter permission errors:

 ## Creating Your First Knowledge Note

-1. **Start the sync process** in a Terminal window:
-   ```bash
-   basic-memory sync --watch
-   ```
-   Keep this running in the background.
+1. **Open Claude Desktop** and start a new conversation.

-2. **Open Claude Desktop** and start a new conversation.
-
-3. **Have a natural conversation** about any topic:
+2. **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..."
   ```

-4. **Ask Claude to create a note**:
+3. **Ask Claude to create a note**:
   ```
   You: "Could you create a note summarizing what we've discussed about coffee brewing?"
   ```

-5. **Confirm note creation**:
+4. **Confirm note creation**:
   Claude will confirm when the note has been created and where it's stored.

-6. **View the created file** in your `~/basic-memory` directory using any text editor or Obsidian.
+5. **View the created file** in your `~/basic-memory` directory using any text editor or Obsidian.
   The file structure will look similar to:
   ```markdown
   ---
@@ -160,6 +180,12 @@ 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:
@@ -245,15 +271,15 @@ basic-memory import claude conversations
 basic-memory import chatgpt
 ```

-After importing, run `basic-memory sync` to index everything.
+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`.

 ## Quick Tips

- Keep `basic-memory sync --watch` running in a terminal window
+- Basic Memory will sync changes from your project in real time.
 - 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 when you need precise context
- Use git to version control your knowledge base
+- 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)
 - Review and edit AI-generated notes for accuracy

 ## Next Steps
@@ -144,7 +144,19 @@ permalink: auth-approaches-2024
 ---
 ```

-If not specified, one will be generated automatically from the title.
+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
+}
+```

 ### Using memory:// URLs

@@ -196,7 +196,7 @@ flowchart TD
    end
    
    BMCP <-->|"write_note() read_note()"| KnowledgeFiles
-    BMCP <-->|"search() build_context()"| KnowledgeIndex
+    BMCP <-->|"search_notes() build_context()"| KnowledgeIndex
    KnowledgeFiles <-.->|Sync Process| KnowledgeIndex
    KnowledgeFiles <-->|Direct Editing| Editors((Text Editors & Git))
    
@@ -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())
+        config = json.loads(config_path.read_text(encoding="utf-8"))
    else:
        config = {"mcpServers": {}}

@@ -0,0 +1,128 @@
+# 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/).
@@ -1,6 +1,6 @@
 [project]
 name = "basic-memory"
-version = "0.10.0"
+version = "0.12.2"
 description = "Local-first knowledge management combining Zettelkasten with knowledge graphs"
 readme = "README.md"
 requires-python = ">=3.12.1"
@@ -40,6 +40,7 @@ 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"]
@@ -1,3 +1,3 @@
 """basic-memory - Local-first knowledge management combining Zettelkasten with knowledge graphs"""

-__version__ = "0.10.0"
+__version__ = "0.12.2"
@@ -7,16 +7,24 @@ from fastapi.exception_handlers import http_exception_handler
 from loguru import logger

 from basic_memory import db
-from basic_memory.config import config as app_config
-from basic_memory.api.routers import knowledge, search, memory, resource, project_info
+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


@asynccontextmanager
 async def lifespan(app: FastAPI):  # pragma: no cover
    """Lifecycle manager for the FastAPI app."""
-    await db.run_migrations(app_config)
+    # Initialize database and file sync services
+    watch_task = await initialize_app(project_config)
+
+    # proceed with startup
    yield
+
    logger.info("Shutting down Basic Memory API")
+    if watch_task:
+        watch_task.cancel()
+
    await db.shutdown_db()


@@ -1,18 +1,17 @@
-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()


@@ -21,11 +20,12 @@ 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",
+        help="Specify which project to use 1",
        envvar="BASIC_MEMORY_PROJECT",
    ),
    version: Optional[bool] = typer.Option(
@@ -38,6 +38,7 @@ 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
@@ -57,9 +58,13 @@ 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")
@@ -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, project_info
+from . import import_claude_projects, import_chatgpt, tool, project

 __all__ = [
    "status",
@@ -14,5 +14,4 @@ __all__ = [
    "import_chatgpt",
    "tool",
    "project",
-    "project_info",
 ]
@@ -1,10 +1,13 @@
 """Database management commands."""

+import asyncio
+
 import typer
 from loguru import logger

-from basic_memory.alembic import migrations
+from basic_memory import db
 from basic_memory.cli.app import app
+from basic_memory.config import config


@app.command()
@@ -14,7 +17,17 @@ 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...")
-        migrations.reset_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")

        if reindex:
            # Import and run sync
@@ -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) as f:
+        with open(json_path, encoding="utf-8") as f:
            lines = f.readlines()
            progress.update(read_task, total=len(lines))

@@ -1,10 +1,7 @@
 """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
@@ -15,12 +12,24 @@ import basic_memory.mcp.tools  # noqa: F401  # pragma: no cover

@app.command()
 def mcp():  # pragma: no cover
-    """Run the MCP server for Claude Desktop integration."""
-    home_dir = config.home
-    project_name = config.project
+    """Run the MCP server"""
+    from basic_memory.config import config
+    import asyncio
+    from basic_memory.services.initialization import initialize_database

-    logger.info(f"Starting Basic Memory MCP server {basic_memory.__version__}")
-    logger.info(f"Project: {project_name}")
-    logger.info(f"Project directory: {home_dir}")
+    # First, run just the database migrations synchronously
+    asyncio.run(initialize_database(config))

+    # 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()
@@ -1,5 +1,6 @@
 """Command module for basic-memory project management."""

+import asyncio
 import os
 from pathlib import Path

@@ -9,6 +10,12 @@ 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()

@@ -92,12 +99,22 @@ 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."""
+    """Set the default project and activate it for the current session."""
    config_manager = ConfigManager()

    try:
+        # Set the default project
        config_manager.set_default_project(name)
-        console.print(f"[green]Project '{name}' set as default[/green]")
+
+        # 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]")
    except ValueError as e:  # pragma: no cover
        console.print(f"[red]Error: {e}[/red]")
        raise typer.Exit(1)
@@ -117,3 +134,152 @@ 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)
@@ -1,167 +0,0 @@
-"""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)
@@ -70,6 +70,7 @@ 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,
@@ -178,14 +179,14 @@ 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, show_progress=False)
+        await sync_service.sync(config.home)

        # watch changes
        await watch_service.run()  # pragma: no cover
    else:
-        # one time sync - use progress bars for better UX
+        # one time sync
        logger.info("Running one-time sync")
-        knowledge_changes = await sync_service.sync(config.home, show_progress=True)
+        knowledge_changes = await sync_service.sync(config.home)

        # Log results
        duration_ms = int((time.time() - start_time) * 1000)
@@ -236,11 +237,11 @@ def sync(
        if not isinstance(e, typer.Exit):
            logger.exception(
                "Sync command failed",
-                project=config.project,
-                error=str(e),
-                error_type=type(e).__name__,
-                watch_mode=watch,
-                directory=str(config.home),
+                f"project={config.project},"
+                f"error={str(e)},"
+                f"error_type={type(e).__name__},"
+                f"watch_mode={watch},"
+                f"directory={str(config.home)}",
            )
            typer.echo(f"Error during sync: {e}", err=True)
            raise typer.Exit(1)
@@ -2,34 +2,32 @@

 import asyncio
 import sys
-from typing import Optional, List, Annotated
+from typing import Annotated, List, Optional

 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 SearchQuery, SearchItemType
+from basic_memory.schemas.search import SearchItemType

 tool_app = typer.Typer()
-app.add_typer(tool_app, name="tool", help="Direct access to MCP tools via CLI")
+app.add_typer(tool_app, name="tool", help="Access to MCP tools via CLI")


@tool_app.command()
@@ -103,6 +101,7 @@ 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)
@@ -122,6 +121,7 @@ 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(
@@ -154,6 +154,7 @@ 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(
@@ -177,8 +178,8 @@ def recent_activity(
        raise


-@tool_app.command()
-def search(
+@tool_app.command("search-notes")
+def search_notes(
    query: str,
    permalink: Annotated[bool, typer.Option("--permalink", help="Search permalink values")] = False,
    title: Annotated[bool, typer.Option("--title", help="Search title values")] = False,
@@ -189,18 +190,34 @@ def search(
    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:
-        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,
+        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,
+            )
        )
-        results = asyncio.run(mcp_search(query=search_query, page=page, page_size=page_size))
        # Use json module for more controlled serialization
        import json

@@ -1,58 +1,26 @@
 """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
-    status,
-    sync,
    db,
-    import_memory_json,
-    mcp,
+    import_chatgpt,
    import_claude_conversations,
    import_claude_projects,
-    import_chatgpt,
-    tool,
+    import_memory_json,
+    mcp,
    project,
+    status,
+    sync,
+    tool,
 )
-
-
-# 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
-
+from basic_memory.config import config
+from basic_memory.services.initialization import ensure_initialization

 if __name__ == "__main__":  # pragma: no cover
+    # Run initialization if we are starting as a module
+    ensure_initialization(config)
+
+    # start the app
    app()
@@ -5,12 +5,13 @@ import os
 from pathlib import Path
 from typing import Any, Dict, Literal, Optional

-import basic_memory
-from basic_memory.utils import setup_logging
 from loguru import logger
 from pydantic import Field, field_validator
 from pydantic_settings import BaseSettings, SettingsConfigDict

+import basic_memory
+from basic_memory.utils import setup_logging
+
 DATABASE_NAME = "memory.db"
 DATA_DIR_NAME = ".basic-memory"
 CONFIG_FILE_NAME = "config.json"
@@ -34,10 +35,14 @@ class ProjectConfig(BaseSettings):

    # Watch service configuration
    sync_delay: int = Field(
-        default=500, description="Milliseconds to wait after changes before syncing", gt=0
+        default=1000, description="Milliseconds to wait after changes before syncing", gt=0
    )

-    log_level: str = "DEBUG"
+    # 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)",
+    )

    model_config = SettingsConfigDict(
        env_prefix="BASIC_MEMORY_",
@@ -76,6 +81,18 @@ 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",
@@ -193,9 +210,14 @@ 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)
+        return ProjectConfig(
+            home=project_path,
+            project=actual_project_name,
+            update_permalinks_on_move=update_permalinks_on_move,
+        )
    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)
@@ -213,11 +235,48 @@ user_home = Path.home()
 log_dir = user_home / DATA_DIR_NAME
 log_dir.mkdir(parents=True, exist_ok=True)

-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})")
+
+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()
@@ -146,7 +146,9 @@ async def engine_session_factory(
            _session_maker = None


-async def run_migrations(app_config: ProjectConfig, database_type=DatabaseType.FILESYSTEM):
+async def run_migrations(
+    app_config: ProjectConfig, database_type=DatabaseType.FILESYSTEM
+):  # pragma: no cover
    """Run any pending alembic migrations."""
    logger.info("Running database migrations...")
    try:
@@ -104,6 +104,9 @@ 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
@@ -4,21 +4,22 @@ Uses markdown-it with plugins to parse structured data from markdown content.
 """

 from dataclasses import dataclass, field
-from pathlib import Path
 from datetime import datetime
+from pathlib import Path
 from typing import Any, Optional
-import dateparser

-from markdown_it import MarkdownIt
+import dateparser
 import frontmatter
+from markdown_it import MarkdownIt

 from basic_memory.markdown.plugins import observation_plugin, relation_plugin
 from basic_memory.markdown.schemas import (
-    EntityMarkdown,
    EntityFrontmatter,
+    EntityMarkdown,
    Observation,
    Relation,
 )
+from basic_memory.utils import parse_tags

 md = MarkdownIt().use(observation_plugin).use(relation_plugin)

@@ -56,11 +57,11 @@ 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:
@@ -91,25 +92,36 @@ class EntityParser:
    async def parse_file(self, path: Path | str) -> EntityMarkdown:
        """Parse markdown file into EntityMarkdown."""

-        absolute_path = self.base_path / path
-        # Parse frontmatter and content using python-frontmatter
-        post = frontmatter.load(str(absolute_path))
+        # 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

+        # 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)
+
+    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.name)
+        metadata["title"] = post.metadata.get("title", absolute_path.stem)
        metadata["type"] = post.metadata.get("type", "note")
-        metadata["tags"] = parse_tags(post.metadata.get("tags", []))
-
+        tags = parse_tags(post.metadata.get("tags", []))  # pyright: ignore
+        if tags:
+            metadata["tags"] = tags
        # frontmatter
        entity_frontmatter = EntityFrontmatter(
            metadata=post.metadata,
        )
-
        entity_content = parse(post.content)
-
        return EntityMarkdown(
            frontmatter=entity_frontmatter,
            content=post.content,
@@ -42,7 +42,7 @@ class EntityFrontmatter(BaseModel):

    @property
    def tags(self) -> List[str]:
-        return self.metadata.get("tags") if self.metadata else []  # pyright: ignore
+        return self.metadata.get("tags") if self.metadata else None  # pyright: ignore

    @property
    def title(self) -> str:
@@ -1,14 +1,14 @@
 """Utilities for converting between markdown and entity models."""

 from pathlib import Path
-from typing import Optional, Any
+from typing import Any, Optional

 from frontmatter import Post

-from basic_memory.file_utils import has_frontmatter, remove_frontmatter
+from basic_memory.file_utils import has_frontmatter, remove_frontmatter, parse_frontmatter
 from basic_memory.markdown import EntityMarkdown
-from basic_memory.models import Entity, Observation as ObservationModel
-from basic_memory.utils import generate_permalink
+from basic_memory.models import Entity
+from basic_memory.models import Observation as ObservationModel


 def entity_model_from_markdown(
@@ -32,16 +32,13 @@ 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 = permalink
+    model.permalink = markdown.frontmatter.permalink
    model.file_path = str(file_path)
    model.content_type = "text/markdown"
    model.created_at = markdown.created
@@ -77,22 +74,33 @@ async def schema_to_markdown(schema: Any) -> Post:
    """
    # Extract content and metadata
    content = schema.content or ""
-    frontmatter_metadata = dict(schema.entity_metadata or {})
+    entity_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"]:
-        frontmatter_metadata.pop(field, None)
+        entity_metadata.pop(field, None)

-    # Create Post with ordered fields
+    # Create Post with fields ordered by insert order
    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
@@ -19,9 +19,7 @@ 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.parent.parent.parent / "static" / "ai_assistant_guide.md"
-    )
+    guide_doc = Path(__file__).parent.parent / "resources" / "ai_assistant_guide.md"
    content = guide_doc.read_text(encoding="utf-8")
    logger.info(f"Loaded AI assistant guide ({len(content)} chars)")
    return content
@@ -5,19 +5,19 @@ providing context from previous interactions to maintain continuity.
 """

 from textwrap import dedent
-from typing import Optional, Annotated
+from typing import Annotated, Optional

 from loguru import logger
 from pydantic import Field

-from basic_memory.mcp.prompts.utils import format_prompt_context, PromptContext, PromptContextItem
+from basic_memory.mcp.prompts.utils import PromptContext, PromptContextItem, format_prompt_context
 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
+from basic_memory.mcp.tools.search import search_notes
 from basic_memory.schemas.base import TimeFrame
 from basic_memory.schemas.memory import GraphContext
-from basic_memory.schemas.search import SearchQuery, SearchItemType
+from basic_memory.schemas.search import SearchItemType


@mcp.prompt(
@@ -47,8 +47,8 @@ async def continue_conversation(

    # If topic provided, search for it
    if topic:
-        search_results = await search(
-            SearchQuery(text=topic, after_date=timeframe, types=[SearchItemType.ENTITY])
+        search_results = await search_notes(
+            query=topic, after_date=timeframe, entity_types=[SearchItemType.ENTITY]
        )

        # Build context from results
@@ -93,7 +93,7 @@ async def continue_conversation(
        ## Next Steps

        You can:
-        - Explore more with: `search({{"text": "{topic}"}})`
+        - Explore more with: `search_notes({{"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]")`
        
@@ -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 as search_tool
+from basic_memory.mcp.tools.search import search_notes as search_tool
 from basic_memory.schemas.base import TimeFrame
-from basic_memory.schemas.search import SearchQuery, SearchResponse
+from basic_memory.schemas.search import 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(SearchQuery(text=query, after_date=timeframe))
+    search_results = await search_tool(query=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("{query} AND additional_term")`
-        - Exclude terms: `search("{query} NOT exclude_term")`
-        - View more results: `search("{query}", after_date=None)`
+        - 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)`
        - Check recent activity: `recent_activity()`
        
        ## Synthesize and Capture Knowledge
@@ -0,0 +1,413 @@
+# 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
@@ -1,11 +1,37 @@
 """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
+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

 # mcp console logging
-configure_logging(level="INFO")
+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()


 # Create the shared server instance
-mcp = FastMCP("Basic Memory")
+mcp = FastMCP("Basic Memory", log_level="ERROR", lifespan=app_lifespan)
@@ -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
+from basic_memory.mcp.tools.search import search_notes
 from basic_memory.mcp.tools.canvas import canvas

 __all__ = [
@@ -22,6 +22,6 @@ __all__ = [
    "read_content",
    "read_note",
    "recent_activity",
-    "search",
+    "search_notes",
    "write_note",
 ]
@@ -6,10 +6,9 @@ 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
+from basic_memory.mcp.tools.search import search_notes
 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(
@@ -63,7 +62,7 @@ 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(SearchQuery(title=identifier))
+    title_results = await search_notes(query=identifier, search_type="title")

    if title_results and title_results.results:
        result = title_results.results[0]  # Get the first/best match
@@ -87,7 +86,7 @@ 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(SearchQuery(text=identifier))
+    text_results = await search_notes(query=identifier, search_type="text")

    # We didn't find a direct match, construct a helpful error message
    if not text_results or not text_results.results:
@@ -1,77 +1,113 @@
 """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 SearchQuery, SearchResponse
-from basic_memory.mcp.async_client import client
+from basic_memory.schemas.search import SearchItemType, SearchQuery, SearchResponse


@mcp.tool(
-    description="Search across all content in basic-memory, including documents and entities",
+    description="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.
+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.

    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: 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")
+        query: The search query string
        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(SearchQuery(text="project planning"))
+        results = await search_notes("project planning")

        # Boolean AND search (both terms must be present)
-        results = await search(SearchQuery(text="project AND planning"))
+        results = await search_notes("project AND planning")

        # Boolean OR search (either term can be present)
-        results = await search(SearchQuery(text="project OR meeting"))
+        results = await search_notes("project OR meeting")

        # Boolean NOT search (exclude terms)
-        results = await search(SearchQuery(text="project NOT meeting"))
+        results = await search_notes("project NOT meeting")

        # Boolean search with grouping
-        results = await search(SearchQuery(text="(project OR planning) AND notes"))
+        results = await search_notes("(project OR planning) AND notes")

        # Search with type filter
-        results = await search(SearchQuery(
-            text="meeting notes",
+        results = await search_notes(
+            query="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(SearchQuery(
-            text="bug report",
+        results = await search_notes(
+            query="bug report",
            after_date="1 week"
-        ))
+        )

        # Pattern matching on permalinks
-        results = await search(SearchQuery(
-            permalink_match="docs/meeting-*"
-        ))
+        results = await search_notes(
+            query="docs/meeting-*",
+            search_type="permalink"
+        )
    """
-    logger.info(f"Searching for {query}")
+    # 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}")
    response = await call_post(
        client,
        "/search/",
-        json=query.model_dump(),
+        json=search_query.model_dump(),
        params={"page": page, "page_size": page_size},
    )
    return SearchResponse.model_validate(response.json())
@@ -1,6 +1,6 @@
 """Write note tool for Basic Memory MCP server."""

-from typing import Optional, List
+from typing import List, Union

 from loguru import logger

@@ -9,6 +9,13 @@ 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(
@@ -18,7 +25,7 @@ async def write_note(
    title: str,
    content: str,
    folder: str,
-    tags: Optional[List[str]] = None,
+    tags=None,  # Remove type hint completely to avoid schema issues
 ) -> str:
    """Write a markdown note to the knowledge base.

@@ -40,13 +47,14 @@ async def write_note(
        Examples:
        `- depends_on [[Content Parser]] (Need for semantic extraction)`
        `- implements [[Search Spec]] (Initial implementation)`
-        `- This feature extends [[Base Design]] and uses [[Core Utils]]`
+        `- This feature extends [[Base Design]] andst 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: Optional list of tags to categorize the note
+        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")

    Returns:
        A markdown formatted summary of the semantic content, including:
@@ -58,8 +66,10 @@ 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 tags]} if tags else None
+    metadata = {"tags": [f"#{tag}" for tag in tag_list]} if tag_list else None
    entity = Entity(
        title=title,
        folder=folder,
@@ -78,8 +88,10 @@ async def write_note(
    # Format semantic summary based on status code
    action = "Created" if response.status_code == 201 else "Updated"
    summary = [
-        f"# {action} {result.file_path} ({result.checksum[:8] if result.checksum else 'unknown'})",
+        f"# {action} note",
+        f"file_path: {result.file_path}",
        f"permalink: {result.permalink}",
+        f"checksum: {result.checksum[:8] if result.checksum else 'unknown'}",
    ]

    # Count observations by category
@@ -105,8 +117,8 @@ async def write_note(
            summary.append(f"- Unresolved: {unresolved}")
            summary.append("\nUnresolved relations will be retried on next sync.")

-    if tags:
-        summary.append(f"\n## Tags\n- {', '.join(tags)}")
+    if tag_list:
+        summary.append(f"\n## Tags\n- {', '.join(tag_list)}")

    # Log the response with structured data
    logger.info(
@@ -137,8 +137,6 @@ 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)
@@ -270,11 +268,9 @@ 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]:
@@ -4,10 +4,10 @@ import json
 import time
 from dataclasses import dataclass
 from datetime import datetime
-from typing import List, Optional, Any, Dict
+from typing import Any, Dict, List, Optional

 from loguru import logger
-from sqlalchemy import text, Executable, Result
+from sqlalchemy import Executable, Result, text
 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[SearchItemType]] = None,
+        types: Optional[List[str]] = None,
        after_date: Optional[datetime] = None,
-        entity_types: Optional[List[str]] = None,
+        entity_types: Optional[List[SearchItemType]] = None,
        limit: int = 10,
        offset: int = 0,
    ) -> List[SearchIndexRow]:
@@ -174,15 +174,15 @@ class SearchRepository:
            else:
                conditions.append("permalink MATCH :permalink")

-        # Handle type filter
-        if types:
-            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, '$.entity_type') IN ({entity_type_list})")
+            type_list = ", ".join(f"'{t.value}'" for t in entity_types)
+            conditions.append(f"type IN ({type_list})")
+
+        # Handle type filter
+        if types:
+            type_list = ", ".join(f"'{t}'" for t in types)
+            conditions.append(f"json_extract(metadata, '$.entity_type') IN ({type_list})")

        # Handle date filter using datetime() for proper comparison
        if after_date:
@@ -49,8 +49,8 @@ class SearchQuery(BaseModel):
    title: Optional[str] = None  # title only search

    # Optional filters
-    types: Optional[List[SearchItemType]] = None  # Filter by item type
-    entity_types: Optional[List[str]] = None  # Filter by entity type
+    types: Optional[List[str]] = None  # Filter by type
+    entity_types: Optional[List[SearchItemType]] = None  # Filter by entity type
    after_date: Optional[Union[datetime, str]] = None  # Time-based filter

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

        # Get type_id pairs for traversal
@@ -1,24 +1,24 @@
 """Service for managing entities in the database."""

 from pathlib import Path
-from typing import Sequence, List, Optional, Tuple, Union
+from typing import List, Optional, Sequence, 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, Observation, Relation
+from basic_memory.models import Entity as EntityModel
+from basic_memory.models import 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.exceptions import EntityNotFoundError, EntityCreationError
-from basic_memory.services import FileService
-from basic_memory.services import BaseService
+from basic_memory.services import BaseService, FileService
+from basic_memory.services.exceptions import EntityCreationError, EntityNotFoundError
 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)
+        existing = await self.link_resolver.resolve_link(schema.permalink or schema.file_path)

        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.permalink}")
+        logger.debug(f"Creating entity: {schema.title}")

        # Get file path and ensure it's a Path object
        file_path = Path(schema.file_path)
@@ -141,10 +141,20 @@ 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(post, sort_keys=False)
+        final_content = frontmatter.dumps(merged_post, sort_keys=False)
        checksum = await self.file_service.write_file(file_path, final_content)

        # parse entity from file
@@ -220,7 +230,7 @@ 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}")
+        logger.debug(f"Creating entity: {markdown.frontmatter.title} file_path: {file_path}")
        model = entity_model_from_markdown(file_path, markdown)

        # Mark as incomplete because we still need to add relations
@@ -305,7 +315,7 @@ 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}, type: {rel.type}"
+                    f"Skipping duplicate relation {rel.type} from {db_entity.permalink} target: {rel.target}"
                )
                continue

@@ -60,7 +60,7 @@ class FileService:
        Returns:
            Raw content string without metadata sections
        """
-        logger.debug("Reading entity content", entity_id=entity.id, permalink=entity.permalink)
+        logger.debug(f"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)
@@ -0,0 +1,143 @@
+"""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
@@ -46,10 +46,17 @@ 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, types=[SearchItemType.ENTITY]),
+                query=SearchQuery(title=clean_text, entity_types=[SearchItemType.ENTITY]),
            )

            if results:
@@ -181,17 +181,6 @@ 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)
@@ -202,22 +191,13 @@ class SearchService:
            content_stems.append(content)
            content_snippet = f"{content[:250]}"

-        content_stems.extend(self._generate_variants(entity.permalink))
+        if 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(
@@ -1,9 +1,8 @@
 """Service for syncing files between filesystem and database."""

 import os
-
-from dataclasses import dataclass
-from dataclasses import field
+import time
+from dataclasses import dataclass, field
 from datetime import datetime
 from pathlib import Path
 from typing import Dict, Optional, Set, Tuple
@@ -11,13 +10,13 @@ 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
@@ -65,6 +64,7 @@ class SyncService:

    def __init__(
        self,
+        config: ProjectConfig,
        entity_service: EntityService,
        entity_parser: EntityParser,
        entity_repository: EntityRepository,
@@ -72,6 +72,7 @@ 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
@@ -79,145 +80,51 @@ class SyncService:
        self.search_service = search_service
        self.file_service = file_service

-    async def sync(self, directory: Path, show_progress: bool = True) -> SyncReport:
+    async def sync(self, directory: Path) -> SyncReport:
        """Sync all files with database."""

        start_time = time.time()
-        console = None
-        progress = None  # Will be initialized if show_progress is True
-
-        logger.info("Sync operation started", directory=str(directory))
+        logger.info(f"Sync operation started for directory: {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(
-            "Sync changes detected",
-            new_files=len(report.new),
-            modified_files=len(report.modified),
-            deleted_files=len(report.deleted),
-            moved_files=len(report.moves),
+            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)}"
        )

-        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)
+        # 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}"
                )
+            else:
+                await self.handle_move(old_path, new_path)

-            new_task = None
-            if report.new:
-                new_task = progress.add_task(  # pyright: ignore
-                    "[green]Adding new files...", total=len(report.new)
-                )
+        # deleted next
+        for path in report.deleted:
+            await self.handle_delete(path)

-            modify_task = None
-            if report.modified:  # pragma: no cover
-                modify_task = progress.add_task(  # pyright: ignore
-                    "[yellow]Updating modified files...", total=len(report.modified)
-                )
+        # then new and modified
+        for path in report.new:
+            await self.sync_file(path, new=True)

-            # 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)
+        for path in report.modified:
+            await self.sync_file(path, new=False)

-                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()
+        await self.resolve_relations()

        duration_ms = int((time.time() - start_time) * 1000)
        logger.info(
-            "Sync operation completed",
-            directory=str(directory),
-            total_changes=report.total,
-            duration_ms=duration_ms,
+            f"Sync operation completed: directory={directory}, total_changes={report.total}, duration_ms={duration_ms}"
        )

        return report
@@ -226,6 +133,7 @@ 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)
@@ -276,6 +184,7 @@ 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(
@@ -292,10 +201,7 @@ class SyncService:
        """
        try:
            logger.debug(
-                "Syncing file",
-                path=path,
-                is_new=new,
-                is_markdown=self.file_service.is_markdown(path),
+                f"Syncing file path={path} is_new={new} is_markdown={self.file_service.is_markdown(path)}"
            )

            if self.file_service.is_markdown(path):
@@ -307,7 +213,7 @@ class SyncService:
                await self.search_service.index_entity(entity)

                logger.debug(
-                    "File sync completed", path=path, entity_id=entity.id, checksum=checksum
+                    f"File sync completed, path={path}, entity_id={entity.id}, checksum={checksum[:8]}"
                )
            return entity, checksum

@@ -326,54 +232,59 @@ class SyncService:
            Tuple of (entity, checksum)
        """
        # Parse markdown first to get any existing permalink
-        logger.debug("Parsing markdown file", path=path)
+        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
        entity_markdown = await self.entity_parser.parse_file(path)

-        # Resolve permalink - this handles all the cases including conflicts
-        permalink = await self.entity_service.resolve_permalink(path, markdown=entity_markdown)
+        # 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)

-        # 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,
-            )
+            # 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}"
+                )

-            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)
+                entity_markdown.frontmatter.metadata["permalink"] = permalink
+                await self.file_service.update_frontmatter(path, {"permalink": permalink})

        # if the file is new, create an entity
        if new:
            # Create entity with final permalink
-            logger.debug("Creating new entity from markdown", path=path, permalink=permalink)
-
+            logger.debug(f"Creating new entity from markdown, path={path}")
            await self.entity_service.create_entity_from_markdown(Path(path), entity_markdown)

        # otherwise we need to update the entity and observations
        else:
-            logger.debug("Updating entity from markdown", path=path, permalink=permalink)
-
+            logger.debug(f"Updating entity from markdown, path={path}")
            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": checksum})
+        await self.entity_repository.update(entity.id, {"checksum": final_checksum})

        logger.debug(
-            "Markdown sync completed",
-            path=path,
-            entity_id=entity.id,
-            observation_count=len(entity.observations),
-            relation_count=len(entity.relations),
+            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]}"
        )

-        return entity, checksum
+        # Return the final checksum to ensure everything is consistent
+        return entity, final_checksum

    async def sync_regular_file(self, path: str, new: bool = True) -> Tuple[Optional[Entity], str]:
        """Sync a non-markdown file with basic tracking.
@@ -414,7 +325,7 @@ class SyncService:
        else:
            entity = await self.entity_repository.get_by_file_path(path)
            if entity is None:  # pragma: no cover
-                logger.error("Entity not found for existing file", path=path)
+                logger.error(f"Entity not found for existing file, path={path}")
                raise ValueError(f"Entity not found for existing file: {path}")

            updated = await self.entity_repository.update(
@@ -422,7 +333,7 @@ class SyncService:
            )

            if updated is None:  # pragma: no cover
-                logger.error("Failed to update entity", entity_id=entity.id, path=path)
+                logger.error(f"Failed to update entity, entity_id={entity.id}, path={path}")
                raise ValueError(f"Failed to update entity with ID {entity.id}")

            return updated, checksum
@@ -434,10 +345,7 @@ class SyncService:
        entity = await self.entity_repository.get_by_file_path(file_path)
        if entity:
            logger.info(
-                "Deleting entity",
-                file_path=file_path,
-                entity_id=entity.id,
-                permalink=entity.permalink,
+                f"Deleting entity with file_path={file_path}, entity_id={entity.id}, permalink={entity.permalink}"
            )

            # Delete from db (this cascades to observations/relations)
@@ -451,10 +359,8 @@ class SyncService:
            )

            logger.debug(
-                "Cleaning up search index",
-                entity_id=entity.id,
-                file_path=file_path,
-                index_entries=len(permalinks),
+                f"Cleaning up search index for entity_id={entity.id}, file_path={file_path}, "
+                f"index_entries={len(permalinks)}"
            )

            for permalink in permalinks:
@@ -464,28 +370,49 @@ class SyncService:
                    await self.search_service.delete_by_entity_id(entity.id)

    async def handle_move(self, old_path, new_path):
-        logger.info("Moving entity", old_path=old_path, new_path=new_path)
+        logger.debug("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 but keep the same permalink for link stability
-            updated = await self.entity_repository.update(entity.id, {"file_path": new_path})
+            # 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)

            if updated is None:  # pragma: no cover
                logger.error(
-                    "Failed to update entity path",
-                    entity_id=entity.id,
-                    old_path=old_path,
-                    new_path=new_path,
+                    "Failed to update entity path"
+                    f"entity_id={entity.id}"
+                    f"old_path={old_path}"
+                    f"new_path={new_path}"
                )
                raise ValueError(f"Failed to update entity path for ID {entity.id}")

            logger.debug(
-                "Entity path updated",
-                entity_id=entity.id,
-                permalink=entity.permalink,
-                old_path=old_path,
-                new_path=new_path,
+                "Entity path updated"
+                f"entity_id={entity.id} "
+                f"permalink={entity.permalink} "
+                f"old_path={old_path} "
+                f"new_path={new_path} "
            )

            # update search index
@@ -500,10 +427,10 @@ class SyncService:

        for relation in unresolved_relations:
            logger.debug(
-                "Attempting to resolve relation",
-                relation_id=relation.id,
-                from_id=relation.from_id,
-                to_name=relation.to_name,
+                "Attempting to resolve relation "
+                f"relation_id={relation.id} "
+                f"from_id={relation.from_id} "
+                f"to_name={relation.to_name}"
            )

            resolved_entity = await self.entity_service.link_resolver.resolve_link(relation.to_name)
@@ -511,12 +438,12 @@ class SyncService:
            # ignore reference to self
            if resolved_entity and resolved_entity.id != relation.from_id:
                logger.debug(
-                    "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,
+                    "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}",
                )
                try:
                    await self.relation_repository.update(
@@ -528,10 +455,10 @@ class SyncService:
                    )
                except IntegrityError:  # pragma: no cover
                    logger.debug(
-                        "Ignoring duplicate relation",
-                        relation_id=relation.id,
-                        from_id=relation.from_id,
-                        to_name=relation.to_name,
+                        "Ignoring duplicate relation "
+                        f"relation_id={relation.id} "
+                        f"from_id={relation.from_id} "
+                        f"to_name={relation.to_name}"
                    )

                # update search index
@@ -549,7 +476,7 @@ class SyncService:
        """
        start_time = time.time()

-        logger.debug("Scanning directory", directory=str(directory))
+        logger.debug(f"Scanning directory {directory}")
        result = ScanResult()

        for root, dirnames, filenames in os.walk(str(directory)):
@@ -571,10 +498,10 @@ class SyncService:

        duration_ms = int((time.time() - start_time) * 1000)
        logger.debug(
-            "Directory scan completed",
-            directory=str(directory),
-            files_found=len(result.files),
-            duration_ms=duration_ms,
+            f"{directory} scan completed "
+            f"directory={str(directory)} "
+            f"files_found={len(result.files)} "
+            f"duration_ms={duration_ms}"
        )

        return result
@@ -70,22 +70,30 @@ class WatchServiceState(BaseModel):


 class WatchService:
-    def __init__(self, sync_service: SyncService, file_service: FileService, config: ProjectConfig):
+    def __init__(
+        self,
+        sync_service: SyncService,
+        file_service: FileService,
+        config: ProjectConfig,
+        quiet: bool = False,
+    ):
        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)
-        self.console = Console()
+
+        # quiet mode for mcp so it doesn't mess up stdout
+        self.console = Console(quiet=quiet)

    async def run(self):  # pragma: no cover
        """Watch for file changes and sync them"""
        logger.info(
            "Watch service started",
-            directory=str(self.config.home),
-            debounce_ms=self.config.sync_delay,
-            pid=os.getpid(),
+            f"directory={str(self.config.home)}",
+            f"debounce_ms={self.config.sync_delay}",
+            f"pid={os.getpid()}",
        )

        self.state.running = True
@@ -111,8 +119,8 @@ class WatchService:
        finally:
            logger.info(
                "Watch service stopped",
-                directory=str(self.config.home),
-                runtime_seconds=int((datetime.now() - self.state.start_time).total_seconds()),
+                f"directory={str(self.config.home)}",
+                f"runtime_seconds={int((datetime.now() - self.state.start_time).total_seconds())}",
            )

            self.state.running = False
@@ -154,7 +162,7 @@ class WatchService:

        start_time = time.time()

-        logger.info("Processing file changes", change_count=len(changes), directory=str(directory))
+        logger.info(f"Processing file changes, change_count={len(changes)}, directory={directory}")

        # Group changes by type
        adds: List[str] = []
@@ -177,9 +185,17 @@ class WatchService:
                modifies.append(relative_path)

        logger.debug(
-            "Grouped file changes", added=len(adds), deleted=len(deletes), modified=len(modifies)
+            f"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()

@@ -223,15 +239,16 @@ 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",
-                            old_path=deleted_path,
-                            new_path=added_path,
-                            error=str(e),
+                            f"old_path={deleted_path}",
+                            f"new_path={added_path}",
+                            f"error={str(e)}",
                        )

        # Handle remaining changes - group them by type for concise output
@@ -247,6 +264,7 @@ 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

@@ -257,28 +275,27 @@ class WatchService:
                full_path = directory / path
                if not full_path.exists() or full_path.is_dir():
                    logger.debug(
-                        "Skipping non-existent or directory path", path=path
+                        f"Skipping non-existent or directory path, path={path}"
                    )  # pragma: no cover
                    processed.add(path)  # pragma: no cover
                    continue  # pragma: no cover

-                logger.debug("Processing new file", path=path)
+                logger.debug(f"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.debug(
-                        "Added file processed",
-                        path=path,
-                        entity_id=entity.id if entity else None,
-                        checksum=checksum,
+                    logger.info(
+                        "new file processed",
+                        f"path={path}",
+                        f"checksum={checksum}",
                    )
                    processed.add(path)
                    add_count += 1
                else:  # pragma: no cover
-                    logger.warning("Error syncing new file", path=path)  # pragma: no cover
+                    logger.warning(f"Error syncing new file, path={path}")  # pragma: no cover
                    self.console.print(
                        f"[orange]?[/orange] Error syncing: {path}"
                    )  # pragma: no cover
@@ -296,7 +313,7 @@ class WatchService:
                    processed.add(path)
                    continue

-                logger.debug("Processing modified file", path=path)
+                logger.debug(f"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
@@ -311,17 +328,18 @@ class WatchService:
                            f"[yellow]...[/yellow] Repeated changes to {path}"
                        )  # pragma: no cover
                else:
-                    # New file being modified
+                    # haven't processed this file
                    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",
-                    path=path,
-                    entity_id=entity.id if entity else None,
-                    checksum=checksum,
+                    "Modified file processed, "
+                    f"path={path} "
+                    f"entity_id={entity.id if entity else None} "
+                    f"checksum={checksum}",
                )
                processed.add(path)

@@ -339,16 +357,17 @@ 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",
-            processed_files=len(processed),
-            total_synced_files=self.state.synced_files,
-            duration_ms=duration_ms,
+            "File change processing completed, "
+            f"processed_files={len(processed)}, "
+            f"total_synced_files={self.state.synced_files}, "
+            f"duration_ms={duration_ms}"
        )

-        await self.write_status()
+        await self.write_status()
@@ -6,7 +6,7 @@ import logging
 import re
 import sys
 from pathlib import Path
-from typing import Optional, Protocol, Union, runtime_checkable
+from typing import Optional, Protocol, Union, runtime_checkable, List

 from loguru import logger
 from unidecode import unidecode
@@ -128,3 +128,37 @@ 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 []
@@ -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(
+results = await search_notes(
    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() to find relevant notes]
+   [Use search_notes() 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("travel")
+    search_results = await search_notes("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("Document")
+       results = await search_notes("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()` or `recent_activity()` to confirm entity titles
+    - **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
@@ -251,7 +251,7 @@ async def test_entity_indexing(client: AsyncClient):

    # Verify it's searchable
    search_response = await client.post(
-        "/search/", json={"text": "search", "types": [SearchItemType.ENTITY.value]}
+        "/search/", json={"text": "search", "entity_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", "types": [SearchItemType.ENTITY.value]}
+        "/search/", json={"text": "delete", "entity_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", "types": [SearchItemType.ENTITY.value]}
+        "/search/", json={"text": "sphinx marker", "entity_types": [SearchItemType.ENTITY.value]}
    )
    results = search_response.json()["results"]
    assert len(results) == 1
@@ -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()
+    file_content = full_path.read_text(encoding="utf-8")
    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()
+    updated_content = full_path.read_text(encoding="utf-8")
    assert json.loads(updated_content) == updated_data

    # Verify entity was updated
@@ -48,11 +48,11 @@ async def test_search_basic_pagination(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 type filter."""
    # Should find with correct type
    response = await client.post(
-        "/search/", json={"text": "test", "types": [SearchItemType.ENTITY.value]}
+        "/search/", json={"text": "test", "entity_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_type_filter(client, indexed_entity):

    # Should find with relation type
    response = await client.post(
-        "/search/", json={"text": "test", "types": [SearchItemType.RELATION.value]}
+        "/search/", json={"text": "test", "entity_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_type_filter(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 entity type filter."""
    # Should find with correct entity type
-    response = await client.post("/search/", json={"text": "test", "entity_types": ["test"]})
+    response = await client.post("/search/", json={"text": "test", "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", "entity_types": ["note"]})
+    response = await client.post("/search/", json={"text": "test", "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",
-            "types": [SearchItemType.ENTITY.value],
-            "entity_types": ["test"],
+            "entity_types": [SearchItemType.ENTITY.value],
+            "types": ["test"],
            "after_date": datetime(2020, 1, 1, tzinfo=timezone.utc).isoformat(),
        },
    )
@@ -3,6 +3,8 @@
 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
@@ -211,7 +213,7 @@ def test_search_basic(cli_env, setup_test_note):
    """Test basic search command."""
    result = runner.invoke(
        tool_app,
-        ["search", "test observation"],
+        ["search-notes", "test observation"],
    )
    assert result.exit_code == 0

@@ -235,7 +237,7 @@ def test_search_permalink(cli_env, setup_test_note):

    result = runner.invoke(
        tool_app,
-        ["search", permalink, "--permalink"],
+        ["search-notes", permalink, "--permalink"],
    )
    assert result.exit_code == 0

@@ -410,3 +412,29 @@ 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
@@ -1,10 +1,11 @@
 """Tests for import_chatgpt command."""

 import json
+
 import pytest
 from typer.testing import CliRunner

-from basic_memory.cli.app import import_app, app
+from basic_memory.cli.app import app, import_app
 from basic_memory.cli.commands import import_chatgpt
 from basic_memory.config import config
 from basic_memory.markdown import EntityParser, MarkdownProcessor
@@ -144,7 +145,7 @@ 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") as f:
+    with open(json_file, "w", encoding="utf-8") as f:
        json.dump([sample_conversation], f)
    return json_file

@@ -167,7 +168,7 @@ async def test_process_chatgpt_json(tmp_path, sample_chatgpt_json):
    assert conv_path.exists()

    # Check content formatting
-    content = conv_path.read_text()
+    content = conv_path.read_text(encoding="utf-8")
    assert "# Test Conversation" in content
    assert "### User" in content
    assert "Hello, this is a test message" in content
@@ -183,14 +184,14 @@ 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") as f:
+    with open(json_file, "w", encoding="utf-8") 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()
+    content = conv_path.read_text(encoding="utf-8")
    assert "```python" in content
    assert "def hello():" in content
    assert "```" in content
@@ -204,7 +205,7 @@ 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") as f:
+    with open(json_file, "w", encoding="utf-8") as f:
        json.dump([sample_conversation_with_hidden], f)

    results = await import_chatgpt.process_chatgpt_json(json_file, tmp_path, processor)
@@ -214,7 +215,7 @@ 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()
+    content = conv_path.read_text(encoding="utf-8")
    assert "Visible message" in content
    assert "Hidden message" not in content

@@ -1,6 +1,7 @@
 """Tests for import_claude command (chat conversations)."""

 import json
+
 import pytest
 from typer.testing import CliRunner

@@ -44,7 +45,7 @@ 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") as f:
+    with open(json_file, "w", encoding="utf-8") as f:
        json.dump([sample_conversation], f)
    return json_file

@@ -65,7 +66,7 @@ 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()
+    content = conv_path.read_text(encoding="utf-8")

    # Check content formatting
    assert "### Human" in content
@@ -156,7 +157,7 @@ def test_import_conversation_with_attachments(tmp_path):
    }

    json_file = tmp_path / "with_attachments.json"
-    with open(json_file, "w") as f:
+    with open(json_file, "w", encoding="utf-8") as f:
        json.dump([conversation], f)

    # Set up environment
@@ -168,7 +169,7 @@ 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()
+    content = conv_path.read_text(encoding="utf-8")
    assert "**Attachment: test.txt**" in content
    assert "```" in content
    assert "Test file content" in content
@@ -1,6 +1,7 @@
 """Tests for import_claude_projects command."""

 import json
+
 import pytest
 from typer.testing import CliRunner

@@ -43,7 +44,7 @@ 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") as f:
+    with open(json_file, "w", encoding="utf-8") as f:
        json.dump([sample_project], f)
    return json_file

@@ -70,14 +71,14 @@ 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()
+    content1 = doc1.read_text(encoding="utf-8")
    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()
+    prompt_content = prompt.read_text(encoding="utf-8")
    assert "# Test Prompt" in prompt_content
    assert "This is a test prompt" in prompt_content

@@ -160,7 +161,7 @@ def test_import_project_without_prompt(tmp_path):
    }

    json_file = tmp_path / "no_prompt.json"
-    with open(json_file, "w") as f:
+    with open(json_file, "w", encoding="utf-8") as f:
        json.dump([project], f)

    # Set up environment
@@ -1,6 +1,7 @@
 """Tests for import_memory_json command."""

 import json
+
 import pytest
 from typer.testing import CliRunner

@@ -35,7 +36,7 @@ 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") as f:
+    with open(json_file, "w", encoding="utf-8") as f:
        for entity in sample_entities:
            f.write(json.dumps(entity) + "\n")
    return json_file
@@ -55,7 +56,7 @@ 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()
+    content = entity_file.read_text(encoding="utf-8")
    assert "Test observation 1" in content
    assert "Test observation 2" in content
    assert "test_relation [[related_entity]]" in content
@@ -120,7 +121,7 @@ def test_import_json_command_handle_old_format(tmp_path):
    ]

    json_file = tmp_path / "old_format.json"
-    with open(json_file, "w") as f:
+    with open(json_file, "w", encoding="utf-8") as f:
        for item in old_format:
            f.write(json.dumps(item) + "\n")

@@ -15,6 +15,13 @@ 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)
@@ -25,6 +32,12 @@ 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():
@@ -123,17 +136,33 @@ 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" in result.stdout
+    assert "Project 'test' set as default and activated" 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))

-    # Set as default
+    # Create the main project directory
+    main_dir = temp_home / "basic-memory"
+    main_dir.mkdir(parents=True, exist_ok=True)
+
+    # Now check the current project
    result = cli_runner.invoke(app, ["project", "current"])
    assert result.exit_code == 0
    assert "Current project: main" in result.stdout
@@ -156,3 +185,24 @@ 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"
@@ -12,7 +12,7 @@ def test_info_stats_command(cli_env, test_graph):
    runner = CliRunner()

    # Run the command
-    result = runner.invoke(cli_app, ["info", "stats"])
+    result = runner.invoke(cli_app, ["project", "info"])

    # 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, ["info", "stats", "--json"])
+    result = runner.invoke(cli_app, ["project", "info", "--json"])

    # Verify exit code
    assert result.exit_code == 0
@@ -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 AsyncSession, AsyncEngine, async_sessionmaker
+from sqlalchemy.ext.asyncio import AsyncEngine, AsyncSession, async_sessionmaker

 from basic_memory import db
 from basic_memory.config import ProjectConfig
@@ -140,6 +140,7 @@ def entity_parser(test_config):

@pytest_asyncio.fixture
 async def sync_service(
+    test_config: ProjectConfig,
    entity_service: EntityService,
    entity_parser: EntityParser,
    entity_repository: EntityRepository,
@@ -149,6 +150,7 @@ 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,
@@ -349,5 +351,5 @@ 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, show_progress=False)
+    await sync_service.sync(test_config.home)
    return test_files
@@ -217,6 +217,37 @@ 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."""
@@ -8,10 +8,10 @@ from pathlib import Path

 import pytest

-from basic_memory.markdown.markdown_processor import MarkdownProcessor, DirtyFileError
+from basic_memory.markdown.markdown_processor import DirtyFileError, MarkdownProcessor
 from basic_memory.markdown.schemas import (
-    EntityMarkdown,
    EntityFrontmatter,
+    EntityMarkdown,
    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()
+    content = path.read_text(encoding="utf-8")
    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()
+    content = path.read_text(encoding="utf-8")

    # 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() + "\nModified!")
+    path.write_text(path.read_text(encoding="utf-8") + "\nModified!")

    # Try to update with old checksum
    update = EntityMarkdown(
@@ -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())
+    content = json.loads(file_path.read_text(encoding="utf-8"))
    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())
+    content = json.loads(file_path.read_text(encoding="utf-8"))
    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())
+    content = json.loads(file_path.read_text(encoding="utf-8"))
    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())
+    content = json.loads(file_path.read_text(encoding="utf-8"))
    assert len(content["nodes"]) == 4
    assert len(content["edges"]) == 2

@@ -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") as mock:
+    with patch("basic_memory.mcp.tools.read_note.search_notes") as mock:
        # Default to empty results
        mock.return_value = SearchResponse(results=[], current_page=1, page_size=1)
        yield mock
@@ -51,8 +51,10 @@ async def test_note_unicode_content(app):

    assert (
        dedent("""
-        # Created test/Unicode Test.md (272389cd)
+        # Created note
+        file_path: test/Unicode Test.md
        permalink: test/unicode-test
+        checksum: 272389cd
        """).strip()
        in result
    )
@@ -201,7 +203,8 @@ 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[0][0].title == "Test Note"
+    assert mock_search.call_args[1]["query"] == "Test Note"
+    assert mock_search.call_args[1]["search_type"] == "title"

    # Verify second lookup was used
    assert mock_call_get.call_count == 2
@@ -254,8 +257,10 @@ 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][0][0].title == "some query"  # Title search
-    assert mock_search.call_args_list[1][0][0].text == "some query"  # Text search
+    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"

    # Verify result contains helpful information
    assert "Note Not Found" in result
@@ -42,6 +42,33 @@ 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.
@@ -4,12 +4,11 @@ import pytest
 from datetime import datetime, timedelta

 from basic_memory.mcp.tools import write_note
-from basic_memory.mcp.tools.search import search
-from basic_memory.schemas.search import SearchQuery, SearchItemType
+from basic_memory.mcp.tools.search import search_notes


@pytest.mark.asyncio
-async def test_search_basic(client):
+async def test_search_text(client):
    """Test basic search functionality."""
    # Create a test note
    result = await write_note(
@@ -21,8 +20,67 @@ async def test_search_basic(client):
    assert result

    # Search for it
-    query = SearchQuery(text="searchable")
-    response = await search(query)
+    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")

    # Verify results
    assert len(response.results) > 0
@@ -42,8 +100,7 @@ async def test_search_pagination(client):
    assert result

    # Search for it
-    query = SearchQuery(text="searchable")
-    response = await search(query, page=1, page_size=1)
+    response = await search_notes(query="searchable", page=1, page_size=1)

    # Verify results
    assert len(response.results) == 1
@@ -61,8 +118,24 @@ async def test_search_with_type_filter(client):
    )

    # Search with type filter
-    query = SearchQuery(text="type", types=[SearchItemType.ENTITY])
-    response = await search(query)
+    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"])

    # Verify all results are entities
    assert all(r.type == "entity" for r in response.results)
@@ -80,8 +153,7 @@ async def test_search_with_date_filter(client):

    # Search with date filter
    one_hour_ago = datetime.now() - timedelta(hours=1)
-    query = SearchQuery(text="recent", after_date=one_hour_ago)
-    response = await search(query)
+    response = await search_notes(query="recent", after_date=one_hour_ago.isoformat())

    # Verify we get results within timeframe
    assert len(response.results) > 0
@@ -1,7 +1,6 @@
 """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
@@ -27,8 +26,10 @@ async def test_write_note(app):
    assert result
    assert (
        dedent("""
-        # Created test/Test Note.md (159f2168)
+        # Created note
+        file_path: test/Test Note.md
        permalink: test/test-note
+        checksum: 159f2168
        
        ## Tags
        - test, documentation
@@ -64,8 +65,10 @@ async def test_write_note_no_tags(app):
    assert result
    assert (
        dedent("""
-        # Created test/Simple Note.md (9a1ff079)
+        # Created note
+        file_path: test/Simple Note.md
        permalink: test/simple-note
+        checksum: 9a1ff079
        """).strip()
        in result
    )
@@ -105,8 +108,10 @@ async def test_write_note_update_existing(app):
    assert result  # Got a valid permalink
    assert (
        dedent("""
-        # Created test/Test Note.md (159f2168)
+        # Created note
+        file_path: test/Test Note.md
        permalink: test/test-note
+        checksum: 159f2168
        
        ## Tags
        - test, documentation
@@ -122,8 +127,10 @@ async def test_write_note_update_existing(app):
    )
    assert (
        dedent("""
-        # Updated test/Test Note.md (a8eb4d44)
+        # Updated note
+        file_path: test/Test Note.md
        permalink: test/test-note
+        checksum: a8eb4d44
        
        ## Tags
        - test, documentation
@@ -187,6 +194,30 @@ 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.
@@ -212,8 +243,10 @@ async def test_write_note_verbose(app):

    assert (
        dedent("""
-        # Created test/Test Note.md (06873a7a)
+        # Created note
+        file_path: test/Test Note.md
        permalink: test/test-note
+        checksum: 06873a7a
        
        ## Observations
        - note: 1
@@ -229,3 +262,118 @@ 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
+    )
@@ -32,12 +32,12 @@ def test_search_filters():
    """Test search result filtering."""
    query = SearchQuery(
        text="search",
-        types=[SearchItemType.ENTITY],
-        entity_types=["component"],
+        entity_types=[SearchItemType.ENTITY],
+        types=["component"],
        after_date=datetime(2024, 1, 1),
    )
-    assert query.types == [SearchItemType.ENTITY]
-    assert query.entity_types == ["component"]
+    assert query.entity_types == [SearchItemType.ENTITY]
+    assert query.types == ["component"]
    assert query.after_date == "2024-01-01T00:00:00"


@@ -6,12 +6,14 @@ 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 EntityNotFoundError, EntityCreationError
+from basic_memory.services.exceptions import EntityCreationError, EntityNotFoundError
 from basic_memory.utils import generate_permalink


@@ -261,7 +263,7 @@ async def test_get_entities_by_permalinks(entity_service: EntityService):


@pytest.mark.asyncio
-async def test_oget_entities_empty_input(entity_service: EntityService):
+async def test_get_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
@@ -521,7 +523,7 @@ async def test_update_with_content(entity_service: EntityService, file_service:
        """
    ).strip()

-    # Create test entity
+    # update entity
    entity, created = await entity_service.create_or_update_entity(
        EntitySchema(
            title="Git Workflow Guide",
@@ -557,3 +559,33 @@ 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
@@ -0,0 +1,49 @@
+"""Tests for the initialization service."""
+
+from unittest.mock import patch
+
+import pytest
+
+from basic_memory.services.initialization import (
+    ensure_initialization,
+    initialize_app,
+    initialize_database,
+)
+
+
+@pytest.mark.asyncio
+@patch("basic_memory.services.initialization.db.run_migrations")
+async def test_initialize_database(mock_run_migrations, test_config):
+    """Test initializing the database."""
+    await initialize_database(test_config)
+    mock_run_migrations.assert_called_once_with(test_config)
+
+
+@pytest.mark.asyncio
+@patch("basic_memory.services.initialization.db.run_migrations")
+async def test_initialize_database_error(mock_run_migrations, test_config):
+    """Test handling errors during database initialization."""
+    mock_run_migrations.side_effect = Exception("Test error")
+    await initialize_database(test_config)
+    mock_run_migrations.assert_called_once_with(test_config)
+
+
+@pytest.mark.asyncio
+@patch("basic_memory.services.initialization.initialize_database")
+@patch("basic_memory.services.initialization.initialize_file_sync")
+async def test_initialize_app(mock_initialize_file_sync, mock_initialize_database, test_config):
+    """Test app initialization."""
+    mock_initialize_file_sync.return_value = "task"
+
+    result = await initialize_app(test_config)
+
+    mock_initialize_database.assert_called_once_with(test_config)
+    mock_initialize_file_sync.assert_called_once_with(test_config)
+    assert result == "task"
+
+
+@patch("basic_memory.services.initialization.asyncio.run")
+def test_ensure_initialization(mock_run, test_config):
+    """Test synchronous initialization wrapper."""
+    ensure_initialization(test_config)
+    mock_run.assert_called_once()
@@ -75,7 +75,7 @@ async def test_search_permalink_wildcard2(search_service, test_graph):
 async def test_search_text(search_service, test_graph):
    """Full-text search"""
    results = await search_service.search(
-        SearchQuery(text="Root Entity", types=[SearchItemType.ENTITY])
+        SearchQuery(text="Root Entity", entity_types=[SearchItemType.ENTITY])
    )
    assert len(results) >= 1
    assert results[0].permalink == "test/root"
@@ -84,7 +84,9 @@ async def test_search_text(search_service, test_graph):
@pytest.mark.asyncio
 async def test_search_title(search_service, test_graph):
    """Title only search"""
-    results = await search_service.search(SearchQuery(title="Root", types=[SearchItemType.ENTITY]))
+    results = await search_service.search(
+        SearchQuery(title="Root", entity_types=[SearchItemType.ENTITY])
+    )
    assert len(results) >= 1
    assert results[0].permalink == "test/root"

@@ -140,7 +142,7 @@ async def test_filters(search_service, test_graph):
    """Test search filters."""
    # Combined filters
    results = await search_service.search(
-        SearchQuery(text="Deep", types=[SearchItemType.ENTITY], entity_types=["deep"])
+        SearchQuery(text="Deep", entity_types=[SearchItemType.ENTITY], types=["deep"])
    )
    assert len(results) == 1
    for r in results:
@@ -179,13 +181,18 @@ async def test_search_type(search_service, test_graph):
    """Test search filters."""

    # Should find only type
-    results = await search_service.search(SearchQuery(types=[SearchItemType.ENTITY]))
+    results = await search_service.search(SearchQuery(types=["test"]))
    assert len(results) > 0
    for r in results:
        assert r.type == SearchItemType.ENTITY

-    # Should find only types passed in
-    results = await search_service.search(SearchQuery(types=[SearchItemType.ENTITY]))
+
+@pytest.mark.asyncio
+async def test_search_entity_type(search_service, test_graph):
+    """Test search filters."""
+
+    # Should find only type
+    results = await search_service.search(SearchQuery(entity_types=[SearchItemType.ENTITY]))
    assert len(results) > 0
    for r in results:
        assert r.type == SearchItemType.ENTITY
@@ -3,8 +3,10 @@
 import asyncio
 from datetime import datetime, timezone
 from pathlib import Path
+from textwrap import dedent

 import pytest
+import pytest_asyncio

 from basic_memory.config import ProjectConfig
 from basic_memory.models import Entity
@@ -44,7 +46,7 @@ type: knowledge
    await create_test_file(project_dir / "source.md", source_content)

    # Initial sync - should create forward reference
-    await sync_service.sync(test_config.home, show_progress=False)
+    await sync_service.sync(test_config.home)

    # Verify forward reference
    source = await entity_service.get_by_permalink("source")
@@ -63,7 +65,7 @@ Target content
    await create_test_file(project_dir / "target_doc.md", target_content)

    # Sync again - should resolve the reference
-    await sync_service.sync(test_config.home, show_progress=False)
+    await sync_service.sync(test_config.home)

    # Verify reference is now resolved
    source = await entity_service.get_by_permalink("source")
@@ -116,7 +118,7 @@ A test concept.
    await entity_service.repository.add(other)

    # Run sync
-    await sync_service.sync(test_config.home, show_progress=False)
+    await sync_service.sync(test_config.home)

    # Verify results
    entities = await entity_service.repository.find_all()
@@ -146,7 +148,7 @@ async def test_sync_hidden_file(
    await create_test_file(project_dir / "concept/.hidden.md", "hidden")

    # Run sync
-    await sync_service.sync(test_config.home, show_progress=False)
+    await sync_service.sync(test_config.home)

    # Verify results
    entities = await entity_service.repository.find_all()
@@ -180,7 +182,7 @@ modified: 2024-01-01
    await create_test_file(project_dir / "concept/depends_on_future.md", content)

    # Sync
-    await sync_service.sync(test_config.home, show_progress=False)
+    await sync_service.sync(test_config.home)

    # Verify entity created but no relations
    entity = await sync_service.entity_service.repository.get_by_permalink(
@@ -236,7 +238,7 @@ modified: 2024-01-01
    await create_test_file(project_dir / "concept/entity_b.md", content_b)

    # Sync
-    await sync_service.sync(test_config.home, show_progress=False)
+    await sync_service.sync(test_config.home)

    # Verify both entities and their relations
    entity_a = await sync_service.entity_service.repository.get_by_permalink("concept/entity-a")
@@ -307,7 +309,7 @@ modified: 2024-01-01
    await create_test_file(project_dir / "concept/duplicate_relations.md", content)

    # Sync
-    await sync_service.sync(test_config.home, show_progress=False)
+    await sync_service.sync(test_config.home)

    # Verify duplicates are handled
    entity = await sync_service.entity_service.repository.get_by_permalink(
@@ -349,7 +351,7 @@ modified: 2024-01-01
    await create_test_file(project_dir / "concept/invalid_category.md", content)

    # Sync
-    await sync_service.sync(test_config.home, show_progress=False)
+    await sync_service.sync(test_config.home)

    # Verify observations
    entity = await sync_service.entity_service.repository.get_by_permalink(
@@ -429,7 +431,7 @@ modified: 2024-01-01
        await create_test_file(project_dir / f"concept/entity_{name}.md", content)

    # Sync
-    await sync_service.sync(test_config.home, show_progress=False)
+    await sync_service.sync(test_config.home)

    # Verify all relations are created correctly regardless of order
    entity_a = await sync_service.entity_service.repository.get_by_permalink("concept/entity-a")
@@ -449,7 +451,7 @@ modified: 2024-01-01
@pytest.mark.asyncio
 async def test_sync_empty_directories(sync_service: SyncService, test_config: ProjectConfig):
    """Test syncing empty directories."""
-    await sync_service.sync(test_config.home, show_progress=False)
+    await sync_service.sync(test_config.home)

    # Should not raise exceptions for empty dirs
    assert (test_config.home).exists()
@@ -484,7 +486,7 @@ modified: 2024-01-01
        doc_path.write_text("Modified during sync")

    # Run sync and modification concurrently
-    await asyncio.gather(sync_service.sync(test_config.home, show_progress=False), modify_file())
+    await asyncio.gather(sync_service.sync(test_config.home), modify_file())

    # Verify final state
    doc = await sync_service.entity_service.repository.get_by_permalink("changing")
@@ -492,7 +494,7 @@ modified: 2024-01-01

    # if we failed in the middle of a sync, the next one should fix it.
    if doc.checksum is None:
-        await sync_service.sync(test_config.home, show_progress=False)
+        await sync_service.sync(test_config.home)
        doc = await sync_service.entity_service.repository.get_by_permalink("changing")
        assert doc.checksum is not None

@@ -528,7 +530,7 @@ Testing permalink generation.
        await create_test_file(test_config.home / filename, content)

        # Run sync
-        await sync_service.sync(test_config.home, show_progress=False)
+        await sync_service.sync(test_config.home)

    # Verify permalinks
    entities = await entity_service.repository.find_all()
@@ -599,7 +601,7 @@ Testing file timestamps
    await create_test_file(file_path, file_dates_content)

    # Run sync
-    await sync_service.sync(test_config.home, show_progress=False)
+    await sync_service.sync(test_config.home)

    # Check explicit frontmatter dates
    explicit_entity = await entity_service.get_by_permalink("explicit-dates")
@@ -639,7 +641,7 @@ Content for move test
    await create_test_file(old_path, content)

    # Initial sync
-    await sync_service.sync(test_config.home, show_progress=False)
+    await sync_service.sync(test_config.home)

    # Move the file
    new_path = project_dir / "new" / "moved_file.md"
@@ -647,7 +649,7 @@ Content for move test
    old_path.rename(new_path)

    # Sync again
-    await sync_service.sync(test_config.home, show_progress=False)
+    await sync_service.sync(test_config.home)

    # Check search index has updated path
    results = await search_service.search(SearchQuery(text="Content for move test"))
@@ -689,7 +691,7 @@ modified: 2024-01-01
    await create_test_file(test_config.home / "concept/incomplete.md", content)

    # Run sync
-    await sync_service.sync(test_config.home, show_progress=False)
+    await sync_service.sync(test_config.home)

    # Verify entity was properly synced
    updated = await entity_service.get_by_permalink("concept/incomplete")
@@ -718,7 +720,7 @@ Content for move test
    await create_test_file(old_path, content)

    # Initial sync
-    await sync_service.sync(test_config.home, show_progress=False)
+    await sync_service.sync(test_config.home)

    # Move the file
    new_path = project_dir / "new" / "moved_file.md"
@@ -726,7 +728,7 @@ Content for move test
    old_path.rename(new_path)

    # Sync again
-    await sync_service.sync(test_config.home, show_progress=False)
+    await sync_service.sync(test_config.home)

    file_content, _ = await file_service.read_file(new_path)
    assert "permalink: old/test-move" in file_content
@@ -745,7 +747,7 @@ Content for move test
    await create_test_file(old_path, content)

    # Sync new file
-    await sync_service.sync(test_config.home, show_progress=False)
+    await sync_service.sync(test_config.home)

    # assert permalink is unique
    file_content, _ = await file_service.read_file(old_path)
@@ -763,11 +765,31 @@ async def test_sync_permalink_resolved_on_update(

    one_file = project_dir / "one.md"
    two_file = project_dir / "two.md"
-    await create_test_file(one_file)
-    await create_test_file(two_file)
+    await create_test_file(
+        one_file,
+        content=dedent(
+            """
+            ---
+            permalink: one
+            ---
+            test content
+            """
+        ),
+    )
+    await create_test_file(
+        two_file,
+        content=dedent(
+            """
+            ---
+            permalink: two
+            ---
+            test content
+            """
+        ),
+    )

    # Run sync
-    await sync_service.sync(test_config.home, show_progress=False)
+    await sync_service.sync(test_config.home)

    # Check permalinks
    file_one_content, _ = await file_service.read_file(one_file)
@@ -790,7 +812,7 @@ test content
    two_file.write_text(updated_content)

    # Run sync
-    await sync_service.sync(test_config.home, show_progress=False)
+    await sync_service.sync(test_config.home)

    # Check permalinks
    file_two_content, _ = await file_service.read_file(two_file)
@@ -811,7 +833,7 @@ test content
    await create_test_file(new_file, new_content)

    # Run another time
-    await sync_service.sync(test_config.home, show_progress=False)
+    await sync_service.sync(test_config.home)

    # Should have deduplicated permalink
    new_file_content, _ = await file_service.read_file(new_file)
@@ -819,7 +841,7 @@ test content


@pytest.mark.asyncio
-async def test_sync_duplicate_observations(
+async def test_sync_permalink_not_created_if_no_frontmatter(
    sync_service: SyncService,
    test_config: ProjectConfig,
    file_service: FileService,
@@ -827,46 +849,79 @@ async def test_sync_duplicate_observations(
    """Test that sync resolves permalink conflicts on update."""
    project_dir = test_config.home

-    content = """
---
-title: a note
-type: note
-tags: []
---
-
-test content
-
- [note] one observation
-"""
-
-    note_file = project_dir / "note.md"
-    await create_test_file(note_file, content)
+    file = project_dir / "one.md"
+    await create_test_file(file)

    # Run sync
-    await sync_service.sync(test_config.home, show_progress=False)
+    await sync_service.sync(test_config.home)

-    # Check permalinks
-    file_one_content, _ = await file_service.read_file(note_file)
-    assert (
-        """---
-title: a note
-type: note
-tags: []
-permalink: note
---
+    # Check permalink not created
+    file_content, _ = await file_service.read_file(file)
+    assert "permalink:" not in file_content

-test content

- [note] one observation
-""".strip()
-        == file_one_content
+@pytest_asyncio.fixture
+def test_config_update_permamlinks_on_move(tmp_path) -> ProjectConfig:
+    """Test configuration using in-memory DB."""
+    config = ProjectConfig(
+        project="test-project",
+        update_permalinks_on_move=True,
    )
+    config.home = tmp_path
+
+    (tmp_path / config.home.name).mkdir(parents=True, exist_ok=True)
+    return config
+
+
+@pytest.mark.asyncio
+async def test_sync_permalink_updated_on_move(
+    test_config_update_permamlinks_on_move: ProjectConfig,
+    sync_service: SyncService,
+    file_service: FileService,
+):
+    """Test that we update a permalink on a file move if set in config ."""
+    test_config = test_config_update_permamlinks_on_move
+    project_dir = test_config.home
+    sync_service.config = test_config
+
+    # Create initial file
+    content = dedent(
+        """
+        ---
+        type: knowledge
+        ---
+        # Test Move
+        Content for move test
+        """
+    )
+
+    old_path = project_dir / "old" / "test_move.md"
+    old_path.parent.mkdir(parents=True)
+    await create_test_file(old_path, content)
+
+    # Initial sync
+    await sync_service.sync(test_config.home)
+
+    # verify permalink
+    old_content, _ = await file_service.read_file(old_path)
+    assert "permalink: old/test-move" in old_content
+
+    # Move the file
+    new_path = project_dir / "new" / "moved_file.md"
+    new_path.parent.mkdir(parents=True)
+    old_path.rename(new_path)
+
+    # Sync again
+    await sync_service.sync(test_config.home)
+
+    file_content, _ = await file_service.read_file(new_path)
+    assert "permalink: new/moved-file" in file_content


@pytest.mark.asyncio
 async def test_sync_non_markdown_files(sync_service, test_config, test_files):
    """Test syncing non-markdown files."""
-    report = await sync_service.sync(test_config.home, show_progress=False)
+    report = await sync_service.sync(test_config.home)
    assert report.total == 2

    # Check files were detected
@@ -889,7 +944,7 @@ async def test_sync_non_markdown_files_modified(
    sync_service, test_config, test_files, file_service
 ):
    """Test syncing non-markdown files."""
-    report = await sync_service.sync(test_config.home, show_progress=False)
+    report = await sync_service.sync(test_config.home)
    assert report.total == 2

    # Check files were detected
@@ -899,7 +954,7 @@ async def test_sync_non_markdown_files_modified(
    test_files["pdf"].write_text("New content")
    test_files["image"].write_text("New content")

-    report = await sync_service.sync(test_config.home, show_progress=False)
+    report = await sync_service.sync(test_config.home)
    assert len(report.modified) == 2

    pdf_file_content, pdf_checksum = await file_service.read_file(test_files["pdf"].name)
@@ -917,7 +972,7 @@ async def test_sync_non_markdown_files_modified(
@pytest.mark.asyncio
 async def test_sync_non_markdown_files_move(sync_service, test_config, test_files):
    """Test syncing non-markdown files updates permalink"""
-    report = await sync_service.sync(test_config.home, show_progress=False)
+    report = await sync_service.sync(test_config.home)
    assert report.total == 2

    # Check files were detected
@@ -925,7 +980,7 @@ async def test_sync_non_markdown_files_move(sync_service, test_config, test_file
    assert test_files["image"].name in [f for f in report.new]

    test_files["pdf"].rename(test_config.home / "moved_pdf.pdf")
-    report2 = await sync_service.sync(test_config.home, show_progress=False)
+    report2 = await sync_service.sync(test_config.home)
    assert len(report2.moves) == 1

    # Verify entity is updated
@@ -937,7 +992,7 @@ async def test_sync_non_markdown_files_move(sync_service, test_config, test_file
@pytest.mark.asyncio
 async def test_sync_non_markdown_files_deleted(sync_service, test_config, test_files):
    """Test syncing non-markdown files updates permalink"""
-    report = await sync_service.sync(test_config.home, show_progress=False)
+    report = await sync_service.sync(test_config.home)
    assert report.total == 2

    # Check files were detected
@@ -945,7 +1000,7 @@ async def test_sync_non_markdown_files_deleted(sync_service, test_config, test_f
    assert test_files["image"].name in [f for f in report.new]

    test_files["pdf"].unlink()
-    report2 = await sync_service.sync(test_config.home, show_progress=False)
+    report2 = await sync_service.sync(test_config.home)
    assert len(report2.deleted) == 1

    # Verify entity is deleted
@@ -964,14 +1019,14 @@ async def test_sync_non_markdown_files_move_with_delete(
    await create_test_file(test_config.home / "other/doc-1.pdf", "content2")

    # Initial sync
-    await sync_service.sync(test_config.home, show_progress=False)
+    await sync_service.sync(test_config.home)

    # First move/delete the original file to make way for the move
    (test_config.home / "doc.pdf").unlink()
    (test_config.home / "other/doc-1.pdf").rename(test_config.home / "doc.pdf")

    # Sync again
-    await sync_service.sync(test_config.home, show_progress=False)
+    await sync_service.sync(test_config.home)

    # Verify the changes
    moved_entity = await sync_service.entity_repository.get_by_file_path("doc.pdf")
@@ -1003,7 +1058,7 @@ tags: []
    await create_test_file(note_file, content)

    # Run sync
-    await sync_service.sync(test_config.home, show_progress=False)
+    await sync_service.sync(test_config.home)

    # Check permalinks
    file_one_content, _ = await file_service.read_file(note_file)
@@ -0,0 +1,63 @@
+"""Test for issue #72 - notes with wikilinks staying in modified status."""
+
+from pathlib import Path
+
+import pytest
+
+from basic_memory.sync.sync_service import SyncService
+
+
+async def create_test_file(path: Path, content: str) -> None:
+    """Create a test file with given content."""
+    path.parent.mkdir(parents=True, exist_ok=True)
+    path.write_text(content)
+
+
+@pytest.mark.asyncio
+async def test_wikilink_modified_status_issue(sync_service: SyncService, test_config):
+    """Test that files with wikilinks don't remain in modified status after sync."""
+    project_dir = test_config.home
+
+    # Create a file with a wikilink
+    content = """---
+title: Test Wikilink
+type: note
+---
+# Test File
+
+This file contains a wikilink to [[another-file]].
+"""
+    test_file_path = project_dir / "test_wikilink.md"
+    await create_test_file(test_file_path, content)
+
+    # Initial sync
+    report1 = await sync_service.sync(test_config.home)
+    assert "test_wikilink.md" in report1.new
+    assert "test_wikilink.md" not in report1.modified
+
+    # Sync again without changing the file - should not be modified
+    report2 = await sync_service.sync(test_config.home)
+    assert "test_wikilink.md" not in report2.new
+    assert "test_wikilink.md" not in report2.modified
+
+    # Create the target file
+    target_content = """---
+title: Another File
+type: note
+---
+# Another File
+
+This is the target file.
+"""
+    target_file_path = project_dir / "another_file.md"
+    await create_test_file(target_file_path, target_content)
+
+    # Sync again after adding target file
+    report3 = await sync_service.sync(test_config.home)
+    assert "another_file.md" in report3.new
+    assert "test_wikilink.md" not in report3.modified
+
+    # Sync one more time - both files should now be stable
+    report4 = await sync_service.sync(test_config.home)
+    assert "test_wikilink.md" not in report4.modified
+    assert "another_file.md" not in report4.modified
@@ -6,8 +6,6 @@ from pathlib import Path
 import pytest
 from watchfiles import Change

-from basic_memory.sync.watch_service import WatchService
-

 async def create_test_file(path: Path, content: str = "test content") -> None:
    """Create a test file with given content."""
@@ -21,9 +19,9 @@ async def test_temp_file_filter(watch_service):
    # Test filter_changes method directly
    tmp_path = str(watch_service.config.home / "test.tmp")
    assert not watch_service.filter_changes(Change.added, tmp_path)
-    
+
    # Test with valid file
-    valid_path = str(watch_service.config.home / "test.md") 
+    valid_path = str(watch_service.config.home / "test.md")
    assert watch_service.filter_changes(Change.added, valid_path)


@@ -31,44 +29,44 @@ async def test_temp_file_filter(watch_service):
 async def test_handle_tmp_files(watch_service, test_config, monkeypatch):
    """Test handling of .tmp files during sync process."""
    project_dir = test_config.home
-    
+
    # Create a .tmp file - this simulates a file being written with write_file_atomic
    tmp_file = project_dir / "test.tmp"
    await create_test_file(tmp_file, "This is a temporary file")
-    
+
    # Create the target final file
    final_file = project_dir / "test.md"
    await create_test_file(final_file, "This is the final file")
-    
+
    # Setup changes that include both the .tmp and final file
    changes = {
        (Change.added, str(tmp_file)),
        (Change.added, str(final_file)),
    }
-    
+
    # Track sync_file calls
    sync_calls = []
-    
+
    # Mock sync_file to track calls
    original_sync_file = watch_service.sync_service.sync_file
-    
+
    async def mock_sync_file(path, new=True):
        sync_calls.append(path)
        return await original_sync_file(path, new)
-    
+
    monkeypatch.setattr(watch_service.sync_service, "sync_file", mock_sync_file)
-    
+
    # Handle changes
    await watch_service.handle_changes(project_dir, changes)
-    
+
    # Verify .tmp file was not processed
    assert "test.tmp" not in sync_calls
    assert "test.md" in sync_calls
-    
+
    # Verify only the final file got an entity
    tmp_entity = await watch_service.sync_service.entity_repository.get_by_file_path("test.tmp")
    final_entity = await watch_service.sync_service.entity_repository.get_by_file_path("test.md")
-    
+
    assert tmp_entity is None, "Temp file should not have an entity"
    assert final_entity is not None, "Final file should have an entity"

@@ -77,44 +75,43 @@ async def test_handle_tmp_files(watch_service, test_config, monkeypatch):
 async def test_atomic_write_tmp_file_handling(watch_service, test_config, monkeypatch):
    """Test handling of file changes during atomic write operations."""
    project_dir = test_config.home
-    
+
    # This test simulates the full atomic write process:
    # 1. First a .tmp file is created
-    # 2. Then the .tmp file is renamed to the final file 
+    # 2. Then the .tmp file is renamed to the final file
    # 3. Both events are processed by the watch service
-    
+
    # Setup file paths
    tmp_path = project_dir / "document.tmp"
    final_path = project_dir / "document.md"
-    
+
    # Create mockup of the atomic write process
    await create_test_file(tmp_path, "Content for document")
-    
+
    # First batch of changes - .tmp file created
    changes1 = {(Change.added, str(tmp_path))}
-    
+
    # Process first batch
    await watch_service.handle_changes(project_dir, changes1)
-    
+
    # Now "replace" the temp file with the final file
    tmp_path.rename(final_path)
-    
+
    # Second batch of changes - .tmp file deleted, final file added
-    changes2 = {
-        (Change.deleted, str(tmp_path)), 
-        (Change.added, str(final_path))
-    }
-    
+    changes2 = {(Change.deleted, str(tmp_path)), (Change.added, str(final_path))}
+
    # Process second batch
    await watch_service.handle_changes(project_dir, changes2)
-    
+
    # Verify only the final file is in the database
    tmp_entity = await watch_service.sync_service.entity_repository.get_by_file_path("document.tmp")
-    final_entity = await watch_service.sync_service.entity_repository.get_by_file_path("document.md")
-    
+    final_entity = await watch_service.sync_service.entity_repository.get_by_file_path(
+        "document.md"
+    )
+
    assert tmp_entity is None, "Temp file should not have an entity"
    assert final_entity is not None, "Final file should have an entity"
-    
+
    # Check events
    new_events = [e for e in watch_service.state.recent_events if e.action == "new"]
    assert len(new_events) == 1
@@ -125,57 +122,63 @@ async def test_atomic_write_tmp_file_handling(watch_service, test_config, monkey
 async def test_rapid_atomic_writes(watch_service, test_config):
    """Test handling of rapid atomic writes to the same destination."""
    project_dir = test_config.home
-    
+
    # This test simulates multiple rapid atomic writes to the same file:
-    # 1. Several .tmp files are created one after another 
+    # 1. Several .tmp files are created one after another
    # 2. Each is then renamed to the same final file
    # 3. Events are batched and processed together
-    
+
    # Setup file paths
    tmp1_path = project_dir / "document.1.tmp"
-    tmp2_path = project_dir / "document.2.tmp" 
+    tmp2_path = project_dir / "document.2.tmp"
    final_path = project_dir / "document.md"
-    
+
    # Create multiple temp files that will be used in sequence
    await create_test_file(tmp1_path, "First version")
    await create_test_file(tmp2_path, "Second version")
-    
+
    # Simulate the first atomic write
    tmp1_path.rename(final_path)
-    
+
    # Brief pause to ensure file system registers the change
    await asyncio.sleep(0.1)
-    
+
    # Read content to verify
-    content1 = final_path.read_text()
+    content1 = final_path.read_text(encoding="utf-8")
    assert content1 == "First version"
-    
+
    # Simulate the second atomic write
    tmp2_path.rename(final_path)
-    
+
    # Verify content was updated
-    content2 = final_path.read_text()
+    content2 = final_path.read_text(encoding="utf-8")
    assert content2 == "Second version"
-    
+
    # Create a batch of changes that might arrive in mixed order
    changes = {
        (Change.added, str(tmp1_path)),
        (Change.deleted, str(tmp1_path)),
-        (Change.added, str(tmp2_path)), 
+        (Change.added, str(tmp2_path)),
        (Change.deleted, str(tmp2_path)),
        (Change.added, str(final_path)),
        (Change.modified, str(final_path)),
    }
-    
+
    # Process all changes
    await watch_service.handle_changes(project_dir, changes)
-    
+
    # Verify only the final file is in the database
-    final_entity = await watch_service.sync_service.entity_repository.get_by_file_path("document.md")
+    final_entity = await watch_service.sync_service.entity_repository.get_by_file_path(
+        "document.md"
+    )
    assert final_entity is not None
-    
+
    # Also verify no tmp entities were created
-    tmp1_entity = await watch_service.sync_service.entity_repository.get_by_file_path("document.1.tmp")
-    tmp2_entity = await watch_service.sync_service.entity_repository.get_by_file_path("document.2.tmp")
+    tmp1_entity = await watch_service.sync_service.entity_repository.get_by_file_path(
+        "document.1.tmp"
+    )
+    tmp2_entity = await watch_service.sync_service.entity_repository.get_by_file_path(
+        "document.2.tmp"
+    )
    assert tmp1_entity is None
    assert tmp2_entity is None
@@ -63,7 +63,7 @@ async def test_write_status(watch_service):
    await watch_service.write_status()

    assert watch_service.status_path.exists()
-    data = json.loads(watch_service.status_path.read_text())
+    data = json.loads(watch_service.status_path.read_text(encoding="utf-8"))
    assert not data["running"]
    assert data["error_count"] == 0

@@ -96,7 +96,7 @@ Test content
    # Verify
    entity = await watch_service.sync_service.entity_repository.get_by_file_path("new_note.md")
    assert entity is not None
-    assert entity.title == "new_note.md"
+    assert entity.title == "new_note"

    # Check event was recorded
    events = [e for e in watch_service.state.recent_events if e.action == "new"]
@@ -125,7 +125,7 @@ Initial content
    await create_test_file(test_file, initial_content)

    # Initial sync
-    await watch_service.sync_service.sync(project_dir, show_progress=False)
+    await watch_service.sync_service.sync(project_dir)

    # Modify file
    modified_content = """---
@@ -169,7 +169,7 @@ Test content
    await create_test_file(test_file, content)

    # Initial sync
-    await watch_service.sync_service.sync(project_dir, show_progress=False)
+    await watch_service.sync_service.sync(project_dir)

    # Delete file
    test_file.unlink()
@@ -207,7 +207,7 @@ Test content
    await create_test_file(old_path, content)

    # Initial sync
-    await watch_service.sync_service.sync(project_dir, show_progress=False)
+    await watch_service.sync_service.sync(project_dir)
    initial_entity = await watch_service.sync_service.entity_repository.get_by_file_path(
        "old/test_move.md"
    )
@@ -306,7 +306,7 @@ type: knowledge
 Test content for rapid moves
 """
    await create_test_file(original_path, content)
-    await watch_service.sync_service.sync(project_dir, show_progress=False)
+    await watch_service.sync_service.sync(project_dir)

    # Perform rapid moves
    temp_path = project_dir / "temp.md"
@@ -393,7 +393,7 @@ This is a test file in a directory
    await create_test_file(file_in_dir, content)

    # Initial sync to add the file to the database
-    await watch_service.sync_service.sync(project_dir, show_progress=False)
+    await watch_service.sync_service.sync(project_dir)

    # Rename the directory
    new_dir_path = project_dir / "new_dir"
@@ -5,16 +5,16 @@ from pathlib import Path
 import pytest

 from basic_memory.file_utils import (
-    compute_checksum,
-    ensure_directory,
-    write_file_atomic,
-    parse_frontmatter,
-    has_frontmatter,
-    remove_frontmatter,
    FileError,
    FileWriteError,
    ParseError,
+    compute_checksum,
+    ensure_directory,
+    has_frontmatter,
+    parse_frontmatter,
+    remove_frontmatter,
    update_frontmatter,
+    write_file_atomic,
 )


@@ -52,7 +52,7 @@ async def test_write_file_atomic(tmp_path: Path):

    await write_file_atomic(test_file, content)
    assert test_file.exists()
-    assert test_file.read_text() == content
+    assert test_file.read_text(encoding="utf-8") == content

    # Temp file should be cleaned up
    assert not test_file.with_suffix(".tmp").exists()
@@ -185,7 +185,7 @@ async def test_update_frontmatter(tmp_path: Path):
    checksum = await update_frontmatter(test_file, updates)

    # Verify content
-    updated = test_file.read_text()
+    updated = test_file.read_text(encoding="utf-8")
    assert "title: Test" in updated
    assert "type: note" in updated
    assert "Test Content" in updated
@@ -204,13 +204,13 @@ async def test_update_frontmatter(tmp_path: Path):
    assert new_checksum != checksum

    # Verify content
-    updated = test_file.read_text()
+    updated = test_file.read_text(encoding="utf-8")
    fm = parse_frontmatter(updated)
    assert fm == {"title": "Test", "type": "doc", "tags": ["test"]}
    assert "Test Content" in updated

    # Test 3: Update with empty dict shouldn't change anything
-    checksum_before = await compute_checksum(test_file.read_text())
+    checksum_before = await compute_checksum(test_file.read_text(encoding="utf-8"))
    new_checksum = await update_frontmatter(test_file, {})
    assert new_checksum == checksum_before

@@ -229,7 +229,7 @@ More content here"""
    test_file.write_text(content)
    await update_frontmatter(test_file, {"title": "Test"})

-    updated = test_file.read_text()
+    updated = test_file.read_text(encoding="utf-8")
    assert remove_frontmatter(updated).strip() == content


@@ -0,0 +1,50 @@
+"""Tests for parse_tags utility function."""
+
+from typing import List, Union
+
+import pytest
+
+from basic_memory.utils import parse_tags
+
+
+@pytest.mark.parametrize(
+    "input_tags,expected",
+    [
+        # None input
+        (None, []),
+        # List inputs
+        ([], []),
+        (["tag1", "tag2"], ["tag1", "tag2"]),
+        (["tag1", "", "tag2"], ["tag1", "tag2"]),  # Empty tags are filtered
+        ([" tag1 ", " tag2 "], ["tag1", "tag2"]),  # Whitespace is stripped
+        # String inputs
+        ("", []),
+        ("tag1", ["tag1"]),
+        ("tag1,tag2", ["tag1", "tag2"]),
+        ("tag1, tag2", ["tag1", "tag2"]),  # Whitespace after comma is stripped
+        ("tag1,,tag2", ["tag1", "tag2"]),  # Empty tags are filtered
+        # Tags with leading '#' characters - these should be stripped
+        (["#tag1", "##tag2"], ["tag1", "tag2"]),
+        ("#tag1,##tag2", ["tag1", "tag2"]),
+        (["tag1", "#tag2", "##tag3"], ["tag1", "tag2", "tag3"]),
+        # Mixed whitespace and '#' characters
+        ([" #tag1 ", " ##tag2 "], ["tag1", "tag2"]),
+        (" #tag1 , ##tag2 ", ["tag1", "tag2"]),
+    ],
+)
+def test_parse_tags(input_tags: Union[List[str], str, None], expected: List[str]) -> None:
+    """Test tag parsing with various input formats."""
+    result = parse_tags(input_tags)
+    assert result == expected
+
+
+def test_parse_tags_special_case() -> None:
+    """Test parsing from non-string, non-list types."""
+
+    # Test with custom object that has __str__ method
+    class TagObject:
+        def __str__(self) -> str:
+            return "tag1,tag2"
+
+    result = parse_tags(TagObject())  # pyright: ignore [reportArgumentType]
+    assert result == ["tag1", "tag2"]
@@ -1,8 +1,9 @@
 """Test permalink formatting during sync."""

-import pytest
 from pathlib import Path

+import pytest
+
 from basic_memory.config import ProjectConfig
 from basic_memory.services import EntityService
 from basic_memory.sync.sync_service import SyncService
@@ -57,7 +58,7 @@ Testing permalink generation.
        await create_test_file(project_dir / filename, content)

    # Run sync
-    await sync_service.sync(test_config.home, show_progress=False)
+    await sync_service.sync(test_config.home)

    # Verify permalinks
    for filename, expected_permalink in test_cases:
@@ -0,0 +1,195 @@
+"""Test UTF-8 character handling in file operations."""
+
+import pytest
+
+from basic_memory import file_utils
+from basic_memory.file_utils import compute_checksum, write_file_atomic
+
+
+@pytest.mark.asyncio
+async def test_write_utf8_characters(tmp_path):
+    """Test writing files with UTF-8 characters."""
+    # Create a test file with various UTF-8 characters
+    test_path = tmp_path / "utf8_test.md"
+
+    # Include characters from various scripts
+    utf8_content = """# UTF-8 Test Document
+    
+## Cyrillic
+Привет мир! (Hello world in Russian)
+
+## Greek
+Γειά σου Κόσμε! (Hello world in Greek)
+
+## Chinese
+你好世界! (Hello world in Chinese)
+
+## Japanese
+こんにちは世界! (Hello world in Japanese)
+
+## Arabic
+مرحبا بالعالم! (Hello world in Arabic)
+
+## Emoji
+🌍 🌎 🌏 🌐 🗺️ 🧭
+"""
+
+    # Test the atomic write function with UTF-8 content
+    await write_file_atomic(test_path, utf8_content)
+
+    # Verify the file was written correctly
+    assert test_path.exists()
+
+    # Read the file back and verify content
+    content = test_path.read_text(encoding="utf-8")
+    assert "Привет мир!" in content
+    assert "Γειά σου Κόσμε!" in content
+    assert "你好世界" in content
+    assert "こんにちは世界" in content
+    assert "مرحبا بالعالم" in content
+    assert "🌍 🌎 🌏" in content
+
+    # Verify checksums match
+    checksum1 = await compute_checksum(utf8_content)
+    checksum2 = await compute_checksum(content)
+    assert checksum1 == checksum2
+
+
+@pytest.mark.asyncio
+async def test_frontmatter_with_utf8(tmp_path):
+    """Test handling of frontmatter with UTF-8 characters."""
+    # Create a test file with frontmatter containing UTF-8
+    test_path = tmp_path / "frontmatter_utf8.md"
+
+    # Create content with UTF-8 in frontmatter
+    content = """---
+title: UTF-8 测试文件 (Test File)
+author: José García
+keywords: 
+  - тестирование
+  - 테스트
+  - 测试
+---
+
+# UTF-8 Support Test
+
+This file has UTF-8 characters in the frontmatter.
+"""
+
+    # Write the file
+    await write_file_atomic(test_path, content)
+
+    # Update frontmatter with more UTF-8
+    await file_utils.update_frontmatter(
+        test_path,
+        {
+            "description": "这是一个测试文件 (This is a test file)",
+            "tags": ["国际化", "юникод", "🔤"],
+        },
+    )
+
+    # Read back and check
+    updated_content = test_path.read_text(encoding="utf-8")
+
+    # Original values should be preserved
+    assert "title: UTF-8 测试文件" in updated_content
+    assert "author: José García" in updated_content
+
+    # New values should be added
+    assert "description: 这是一个测试文件" in updated_content
+    assert "国际化" in updated_content
+    assert "юникод" in updated_content
+    assert "🔤" in updated_content
+
+
+@pytest.mark.asyncio
+async def test_utf8_in_entity_sync(sync_service, test_config):
+    """Test syncing an entity with UTF-8 content."""
+    project_dir = test_config.home
+
+    # Create a test file with UTF-8 characters
+    test_file = project_dir / "utf8_entity.md"
+    utf8_content = """---
+type: knowledge
+permalink: i18n/utf8-document
+---
+# UTF-8 测试文档
+
+## Observations
+- [language] العربية (Arabic) is written right-to-left
+- [language] 日本語 (Japanese) uses three writing systems
+- [encoding] UTF-8 可以编码所有 Unicode 字符
+
+## Relations
+- relates_to [[i18n/Ελληνικά]]
+- relates_to [[i18n/Русский]]
+"""
+
+    # Write the file
+    test_file.parent.mkdir(parents=True, exist_ok=True)
+    test_file.write_text(utf8_content, encoding="utf-8")
+
+    # Sync the file
+    await sync_service.sync(test_config.home)
+
+    # Verify entity was created
+    entity = await sync_service.entity_service.get_by_permalink("i18n/utf8-document")
+    assert entity is not None
+
+    # Verify observations were created with UTF-8 content
+    assert len(entity.observations) == 3
+
+    # Check observation content
+    obs_categories = [o.category for o in entity.observations]
+    obs_content = [o.content for o in entity.observations]
+
+    assert "language" in obs_categories
+    assert "encoding" in obs_categories
+    assert any("العربية" in c for c in obs_content)
+    assert any("日本語" in c for c in obs_content)
+    assert any("Unicode" in c for c in obs_content)
+
+    # Check relations
+    assert len(entity.relations) == 2
+    relation_names = [r.to_name for r in entity.relations]
+    assert "i18n/Ελληνικά" in relation_names
+    assert "i18n/Русский" in relation_names
+
+
+@pytest.mark.asyncio
+async def test_write_file_service_utf8(sync_service, test_config):
+    """Test FileService handling of UTF-8 content."""
+    file_service = sync_service.file_service
+
+    # Test writing UTF-8 content through the file service
+    test_path = "utf8_service_test.md"
+    utf8_content = """---
+title: FileService UTF-8 Test
+---
+# UTF-8 通过 FileService 测试
+
+Testing FileService with UTF-8:
+* Português: Olá mundo!
+* Thai: สวัสดีชาวโลก
+* Korean: 안녕하세요 세계
+* Hindi: नमस्ते दुनिया
+"""
+
+    # Use the file service to write the file
+    checksum = await file_service.write_file(test_path, utf8_content)
+
+    # Verify file exists
+    full_path = file_service.base_path / test_path
+    assert full_path.exists()
+
+    # Read back content and verify
+    content, read_checksum = await file_service.read_file(test_path)
+
+    assert "通过" in content
+    assert "Português" in content
+    assert "สวัสดีชาวโลก" in content
+    assert "안녕하세요" in content
+    assert "नमस्ते" in content
+
+    # Checksums should match
+    assert checksum == read_checksum
@@ -25,16 +25,16 @@ wheels = [

 [[package]]
 name = "alembic"
-version = "1.14.1"
+version = "1.15.1"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
    { name = "mako" },
    { name = "sqlalchemy" },
    { name = "typing-extensions" },
 ]
-sdist = { url = "https://files.pythonhosted.org/packages/99/09/f844822e4e847a3f0bd41797f93c4674cd4d2462a3f6c459aa528cdf786e/alembic-1.14.1.tar.gz", hash = "sha256:496e888245a53adf1498fcab31713a469c65836f8de76e01399aa1c3e90dd213", size = 1918219 }
+sdist = { url = "https://files.pythonhosted.org/packages/4a/ed/901044acb892caa5604bf818d2da9ab0df94ef606c6059fdf367894ebf60/alembic-1.15.1.tar.gz", hash = "sha256:e1a1c738577bca1f27e68728c910cd389b9a92152ff91d902da649c192e30c49", size = 1924789 }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/54/7e/ac0991d1745f7d755fc1cd381b3990a45b404b4d008fc75e2a983516fbfe/alembic-1.14.1-py3-none-any.whl", hash = "sha256:1acdd7a3a478e208b0503cd73614d5e4c6efafa4e73518bb60e4f2846a37b1c5", size = 233565 },
+    { url = "https://files.pythonhosted.org/packages/99/f7/d398fae160568472ddce0b3fde9c4581afc593019a6adc91006a66406991/alembic-1.15.1-py3-none-any.whl", hash = "sha256:197de710da4b3e91cf66a826a5b31b5d59a127ab41bd0fc42863e2902ce2bbbe", size = 231753 },
 ]

 [[package]]
@@ -48,16 +48,16 @@ wheels = [

 [[package]]
 name = "anyio"
-version = "4.8.0"
+version = "4.9.0"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
    { name = "idna" },
    { name = "sniffio" },
    { name = "typing-extensions", marker = "python_full_version < '3.13'" },
 ]
-sdist = { url = "https://files.pythonhosted.org/packages/a3/73/199a98fc2dae33535d6b8e8e6ec01f8c1d76c9adb096c6b7d64823038cde/anyio-4.8.0.tar.gz", hash = "sha256:1d9fe889df5212298c0c0723fa20479d1b94883a2df44bd3897aa91083316f7a", size = 181126 }
+sdist = { url = "https://files.pythonhosted.org/packages/95/7d/4c1bd541d4dffa1b52bd83fb8527089e097a106fc90b467a7313b105f840/anyio-4.9.0.tar.gz", hash = "sha256:673c0c244e15788651a4ff38710fea9675823028a6f08a5eda409e0c9840a028", size = 190949 }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/46/eb/e7f063ad1fec6b3178a3cd82d1a3c4de82cccf283fc42746168188e1cdd5/anyio-4.8.0-py3-none-any.whl", hash = "sha256:b5011f270ab5eb0abf13385f851315585cc37ef330dd88e27ec3d34d651fd47a", size = 96041 },
+    { url = "https://files.pythonhosted.org/packages/a1/ee/48ca1a7c89ffec8b6a0c5d02b89c305671d5ffd8d3c94acf8b8c408575bb/anyio-4.9.0-py3-none-any.whl", hash = "sha256:9f76d541cad6e36af7beb62e978876f3b41e3e04f2c1fbf0884604c0a9c4d93c", size = 100916 },
 ]

 [[package]]
@@ -71,7 +71,7 @@ wheels = [

 [[package]]
 name = "basic-memory"
-version = "0.9.0"
+version = "0.12.1"
 source = { editable = "." }
 dependencies = [
    { name = "aiosqlite" },
@@ -148,6 +148,15 @@ dev = [
    { name = "ruff", specifier = ">=0.1.6" },
 ]

+[[package]]
+name = "cabarchive"
+version = "0.2.4"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/28/d3/a544aed878edc269ce4427bc937310b73624e1d595de7f4e5bcab413a639/cabarchive-0.2.4.tar.gz", hash = "sha256:04f60089473114cf26eab2b7e1d09611c5bfaf8edd3202dacef66bb5c71e48cf", size = 21064 }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/0f/fb/713421f46c68f4bf9cd26f05bda0c233446108997b6b4d83d7ef07f20009/cabarchive-0.2.4-py3-none-any.whl", hash = "sha256:4afabd224eb2e40af8e907379fb8eec6b0adfb71c2aef4457ec3a4d77383c059", size = 25729 },
+]
+
 [[package]]
 name = "certifi"
 version = "2025.1.31"
@@ -195,66 +204,78 @@ wheels = [

 [[package]]
 name = "coverage"
-version = "7.6.12"
+version = "7.7.1"
 source = { registry = "https://pypi.org/simple" }
-sdist = { url = "https://files.pythonhosted.org/packages/0c/d6/2b53ab3ee99f2262e6f0b8369a43f6d66658eab45510331c0b3d5c8c4272/coverage-7.6.12.tar.gz", hash = "sha256:48cfc4641d95d34766ad41d9573cc0f22a48aa88d22657a1fe01dca0dbae4de2", size = 805941 }
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 [[package]]
Author	SHA1	Message	Date
semantic-release	9433065a57	chore(release): 0.12.2 [skip ci]	2025-04-08 16:27:42 +00:00
Paul Hernandez	2934176331	fix: utf8 for all file reads/write/open instead of default platform encoding (#91 ) Signed-off-by: phernandez <paul@basicmachines.co>	2025-04-08 10:55:01 -05:00
semantic-release	ac89eb47cb	chore(release): 0.12.1 [skip ci]	2025-04-07 22:47:23 +00:00
Paul Hernandez	78a3412bcf	fix: run migrations and sync when starting mcp (#88 )	2025-04-07 17:45:26 -05:00
Paul Hernandez	fa314b5d2b	Update README.md Signed-off-by: Paul Hernandez <60959+phernandez@users.noreply.github.com>	2025-04-06 20:29:00 -05:00
Paul Hernandez	d2ac62a27c	Update README.md Signed-off-by: Paul Hernandez <60959+phernandez@users.noreply.github.com>	2025-04-06 20:25:06 -05:00
semantic-release	7ce7a29f35	chore(release): 0.12.0 [skip ci]	2025-04-06 23:44:17 +00:00
Paul Hernandez	3f4d9e4d87	fix: write_note preserves frontmatter fields in content (#84 )	2025-04-06 18:39:51 -05:00
Paul Hernandez	00c8633cfc	feat: add watch to mcp process (#83 )	2025-04-06 18:33:10 -05:00
Paul Hernandez	617e60bda4	feat: permalink enhancements (#82 ) - Avoiding "useless permalink values" for files without metadata - Enable permalinks to be updated on move via config setting	2025-04-06 14:54:59 -05:00
github-actions[bot]	6c19c9edf5	fix: [BUG] `#` character accumulation in markdown frontmatter tags prop (#79 )	2025-04-05 23:07:53 -05:00
github-actions[bot]	9bff1f732e	fix: [BUG] write_note Tool Fails to Update Existing Files in Some Situations. (#80 )	2025-04-05 22:31:40 -05:00
Paul Hernandez	248214cb11	fix: set default mcp log level to ERROR (#81 )	2025-04-05 22:27:29 -05:00
Jason Noble	40ea28b0bf	docs: Updated basicmachines.co links to be https (#69 )	2025-04-05 22:22:37 -05:00
Marc Baiza	43cbb7b38c	docs: Add VS Code instructions to README (#76 )	2025-04-05 22:18:56 -05:00
github-actions[bot]	7930ddb291	fix: [BUG] Some notes never exit "modified" status (#77 )	2025-04-05 22:03:38 -05:00
phernandez	1844e58210	Add pull_request_target trigger to test workflow with explanatory comment	2025-04-05 20:30:05 -05:00
phernandez	7fbb5ebfc5	Update claude-code-github-action to v0.11.0 with backtick handling fix	2025-04-05 20:04:18 -05:00
phernandez	0e5a465b10	add claude-output to .gitignore Signed-off-by: phernandez <paul@basicmachines.co>	2025-04-05 19:45:07 -05:00
github-actions[bot]	9d581cee13	fix: [BUG] Cursor has errors calling search tool (#78 )	2025-04-05 19:12:23 -05:00
phernandez	f58852954b	Update to claude-code-github-action v0.10.0 to check comment author for org membership	2025-04-05 12:54:33 -05:00
phernandez	edd426b99f	Update to claude-code-github-action v0.9.0 with organization membership check fix	2025-04-05 12:42:35 -05:00
phernandez	6b4a421315	Update to claude-code-github-action v0.8.0 with PERSONAL_ACCESS_TOKEN support	2025-04-05 12:13:05 -05:00
phernandez	4632405446	Fix claude-code-actions.yml to use v0.7.0 of basicmachines-co action	2025-04-05 12:01:04 -05:00
phernandez	3a6d5ff58d	update claude code actions Signed-off-by: phernandez <paul@basicmachines.co>	2025-04-04 23:31:08 -05:00
phernandez	03de85ec32	add claude code github action workflow Signed-off-by: phernandez <paul@basicmachines.co>	2025-04-04 21:20:40 -05:00
phernandez	084c91ecce	update basic-memory dep version Signed-off-by: phernandez <paul@basicmachines.co>	2025-03-30 17:46:44 -05:00
semantic-release	3d45227b72	chore(release): 0.11.0 [skip ci]	2025-03-29 00:19:46 +00:00
Paul Hernandez	069c0a21c6	feat: add bm command alias for basic-memory (#67 ) Signed-off-by: phernandez <paul@basicmachines.co>	2025-03-28 19:12:25 -05:00
Paul Hernandez	b27827671d	feat: rename search tool to search_notes (#66 ) Signed-off-by: phernandez <paul@basicmachines.co>	2025-03-28 19:11:35 -05:00
Paul Hernandez	0743ade5fc	fix: just delete db for reset db instead of using migrations. (#65 ) Signed-off-by: phernandez <paul@basicmachines.co>	2025-03-28 19:11:11 -05:00
Paul Hernandez	f1c95709cb	fix: make logs for each process - mcp, sync, cli (#64 ) Signed-off-by: phernandez <paul@basicmachines.co>	2025-03-28 19:10:43 -05:00
Matias Forbord	3c68b7d5dd	docs: Update broken "Multiple Projects" link in README.md (#55 )	2025-03-26 14:31:51 -05:00
semantic-release	3d0077990f	chore(release): 0.10.1 [skip ci]	2025-03-25 18:12:28 +00:00
phernandez	731b502d36	docs: add help docs to mcp cli tools Signed-off-by: phernandez <paul@basicmachines.co>	2025-03-25 13:01:11 -05:00
phernandez	2a881b1425	refactor: move project stats into projct subcommand Signed-off-by: phernandez <paul@basicmachines.co>	2025-03-25 12:50:11 -05:00
phernandez	681af5d450	chore: remove duplicate code in entity_service.py from bad merge Signed-off-by: phernandez <paul@basicmachines.co>	2025-03-25 12:27:37 -05:00
phernandez	b35037eb86	fix broken merge Signed-off-by: phernandez <paul@basicmachines.co>	2025-03-24 23:18:22 -05:00
phernandez	b667bca5a2	fix test coverage and type checks Signed-off-by: phernandez <paul@basicmachines.co>	2025-03-24 22:46:47 -05:00
phernandez	e716946b44	fix: preserve custom frontmatter fields when updating notes 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>	2025-03-24 22:46:47 -05:00
phernandez	46c4fd2164	fix: make set_default_project also activate project for current session to fix #37 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>	2025-03-24 22:46:47 -05:00
phernandez	9c791259a0	\fix: improve tags handling in write_note tool to fix #38\n\nThis change makes the write_note tool more flexible with tag inputs by:\n1. Adding a parse_tags helper function to handle various input formats\n2. Removing explicit type annotation from the write_note signature\n3. Adding documentation on how to pass tags from external MCP clients\n4. Adding a test that reproduces the issue from bug report #38\n\nThe issue occurred in external MCP clients like Cursor where the tags\nparameter was causing type mismatch errors.\n\n\ud83e\udd16 Generated with [Claude Code](https://claude.ai/code )\n\nCo-Authored-By: Claude <noreply@anthropic.com>\ Signed-off-by: phernandez <paul@basicmachines.co>	2025-03-24 22:46:47 -05:00
phernandez	cc2cae72c1	fix: move ai_assistant_guide.md into package resources to fix #39 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>	2025-03-24 22:46:47 -05:00
phernandez	0a1fdd8f15	update docs Signed-off-by: phernandez <paul@basicmachines.co>	2025-03-24 22:46:47 -05:00
phernandez	78f234b180	fix: preserve custom frontmatter fields when updating notes 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>	2025-03-24 19:50:38 -05:00
phernandez	cbe72be10a	fix: make set_default_project also activate project for current session to fix #37 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>	2025-03-24 18:56:51 -05:00
phernandez	0ade6b0603	\fix: improve tags handling in write_note tool to fix #38\n\nThis change makes the write_note tool more flexible with tag inputs by:\n1. Adding a parse_tags helper function to handle various input formats\n2. Removing explicit type annotation from the write_note signature\n3. Adding documentation on how to pass tags from external MCP clients\n4. Adding a test that reproduces the issue from bug report #38\n\nThe issue occurred in external MCP clients like Cursor where the tags\nparameter was causing type mismatch errors.\n\n\ud83e\udd16 Generated with [Claude Code](https://claude.ai/code )\n\nCo-Authored-By: Claude <noreply@anthropic.com>\	2025-03-24 18:30:21 -05:00
phernandez	390ff9d31c	fix: move ai_assistant_guide.md into package resources to fix #39 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>	2025-03-24 17:34:47 -05:00
phernandez	3ed74b4a4d	update docs	2025-03-24 17:28:30 -05:00
Ikko Eltociear Ashimine	dfaf0fea9c	docs: update CLAUDE.md (#33 ) fix spelling in CLAUDE.md: enviroment -> environment Signed-off-by: Ikko Eltociear Ashimine <eltociear@gmail.com>	2025-03-24 13:15:12 -05:00
phernandez	b26afa927f	docs: add mcp badge, update cli reference, llms-install.md Signed-off-by: phernandez <paul@basicmachines.co>	2025-03-16 14:09:08 -05:00
phernandez	3806943f8c	add star history to README.md Signed-off-by: phernandez <paul@basicmachines.co>	2025-03-16 11:24:08 -05:00
phernandez	3bffb2e190	Add updated getting started docs and utf8 test Signed-off-by: phernandez <paul@basicmachines.co>	2025-03-15 16:52:17 -05:00