test(mcp): cover write-note overwrite conflict integration

Signed-off-by: phernandez <paul@basicmachines.co>

docs/cloud-cli.md

@@ -1,6 +1,6 @@
 # Basic Memory Cloud CLI Guide
 
-The Basic Memory Cloud CLI provides seamless integration between local and cloud knowledge bases using **project-scoped synchronization**. Personal workspaces can optionally use local rclone mirrors, giving you fine-grained control over what syncs and where.
+The Basic Memory Cloud CLI provides seamless integration between local and cloud knowledge bases using **project-scoped synchronization**. Each project can optionally sync with the cloud, giving you fine-grained control over what syncs and where.
 
 ## Overview
 
@@ -8,13 +8,9 @@ The cloud CLI enables you to:
 - **Authenticate cloud access** - OAuth/API key credentials are stored locally for cloud operations
 - **Project-scoped sync** - Each project independently manages its sync configuration
 - **Explicit operations** - Sync only what you want, when you want
-- **Bidirectional sync** - Keep Personal workspace local mirrors and cloud in sync with rclone bisync
+- **Bidirectional sync** - Keep local and cloud in sync with rclone bisync
 - **Offline access** - Work locally, sync when ready
 
-Team workspaces are accessed through the cloud API/MCP and do not support local
-multi-user rclone sync/bisync. Use `bm project list --workspace <workspace>` to
-inspect Team projects.
-
 ## Prerequisites
 
 Before using Basic Memory Cloud, you need:
@@ -43,7 +39,7 @@ If you attempt to log in without an active subscription, you'll receive a "Subsc
 **Projects can exist in three states:**
 
 1. **Cloud-only** - Project exists on cloud, no local copy
-2. **Cloud + Local (synced)** - Personal workspace project has a local working directory that syncs
+2. **Cloud + Local (synced)** - Project has a local working directory that syncs
 3. **Local-only** - Project exists locally and is not routed to cloud
 
 **Example:**
@@ -59,8 +55,8 @@ bm project add work --cloud --local-path ~/work-notes
 bm project add temp --cloud  # No local sync
 
 # Now you can sync individually (after initial --resync):
-bm cloud bisync --name research
-bm cloud bisync --name work
+bm project bisync --name research
+bm project bisync --name work
 # temp stays cloud-only
 ```
 
@@ -91,7 +87,7 @@ Apply OSS discount code `{{OSS_DISCOUNT_CODE}}` during checkout to receive 20% o
 
 ### 2. Set Up Sync
 
-Install rclone and configure Personal workspace sync credentials:
+Install rclone and configure credentials:
 
 ```bash
 bm cloud setup
@@ -103,7 +99,7 @@ bm cloud setup
 3. Generates scoped S3 credentials for sync
 4. Configures single rclone remote: `basic-memory-cloud`
 
-**Result:** You're ready to sync Personal workspace projects. No sync directories created yet - those come with project setup.
+**Result:** You're ready to sync projects. No sync directories created yet - those come with project setup.
 
 Rclone setup uses package managers such as Homebrew, MacPorts, apt, dnf, yum, pacman,
 zypper, snap, winget, Chocolatey, or Scoop when available. It does not run remote
@@ -112,7 +108,7 @@ manual install instructions.
 
 ### 3. Add Projects with Sync
 
-Create Personal workspace projects with optional local sync paths:
+Create projects with optional local sync paths:
 
 ```bash
 # Create cloud project without local sync
@@ -141,10 +137,10 @@ Establish the initial sync baseline. **Best practice:** Always preview with `--d
 
 ```bash
 # Step 1: Preview the initial sync (recommended)
-bm cloud bisync --name research --resync --dry-run
+bm project bisync --name research --resync --dry-run
 
 # Step 2: If all looks good, run the actual sync
-bm cloud bisync --name research --resync
+bm project bisync --name research --resync
 ```
 
 **What happens under the covers:**
@@ -171,7 +167,7 @@ This will effectively make both Path1 and Path2 filesystems contain a matching s
 After the first sync, just run bisync without `--resync`:
 
 ```bash
-bm cloud bisync --name research
+bm project bisync --name research
 ```
 
 **What happens:**
@@ -239,7 +235,7 @@ bm project add research --cloud --local-path ~/Documents/research
 - Stores sync config in `~/.basic-memory/config.json`
 - Prepares for bisync (but doesn't sync yet)
 
-**Result:** Project ready to sync. Run `bm cloud bisync --name research --resync` to establish baseline.
+**Result:** Project ready to sync. Run `bm project bisync --name research --resync` to establish baseline.
 
 **Use case 3: Add sync to existing cloud project**
 
@@ -296,24 +292,20 @@ For MCP stdio, routing is always local.
 
 ## File Synchronization
 
-Local rclone sync/bisync is supported only for Personal workspaces. Team
-workspaces are cloud-only for local CLI usage; access them through cloud API/MCP
-routing instead of a local multi-user rclone mirror.
-
 ### Understanding the Sync Commands
 
 **There are three sync-related commands:**
 
-1. `bm cloud sync` - One-way: local → cloud (make cloud match local)
-2. `bm cloud bisync` - Two-way: local ↔ cloud (recommended)
-3. `bm cloud check` - Verify files match (no changes)
+1. `bm project sync` - One-way: local → cloud (make cloud match local)
+2. `bm project bisync` - Two-way: local ↔ cloud (recommended)
+3. `bm project check` - Verify files match (no changes)
 
 ### One-Way Sync: Local → Cloud
 
 **Use case:** You made changes locally and want to push to cloud (overwrite cloud).
 
 ```bash
-bm cloud sync --name research
+bm project sync --name research
 ```
 
 **What happens:**
@@ -335,10 +327,10 @@ bm cloud sync --name research
 
 ```bash
 # First time - establish baseline
-bm cloud bisync --name research --resync
+bm project bisync --name research --resync
 
 # Subsequent syncs
-bm cloud bisync --name research
+bm project bisync --name research
 ```
 
 **What happens:**
@@ -357,7 +349,7 @@ echo "Local change" > ~/Documents/research/notes.md
 # Cloud now has: "Cloud change"
 
 # Run bisync
-bm cloud bisync --name research
+bm project bisync --name research
 
 # Result: Newer file wins (based on modification time)
 # If cloud was more recent, cloud version kept
@@ -374,7 +366,7 @@ bm cloud bisync --name research
 **Use case:** Check if local and cloud match without making changes.
 
 ```bash
-bm cloud check --name research
+bm project check --name research
 ```
 
 **What happens:**
@@ -386,7 +378,7 @@ bm cloud check --name research
 
 ```bash
 # One-way check (faster)
-bm cloud check --name research --one-way
+bm project check --name research --one-way
 ```
 
 ### Preview Changes (Dry Run)
@@ -394,7 +386,7 @@ bm cloud check --name research --one-way
 **Use case:** See what would change without actually syncing.
 
 ```bash
-bm cloud bisync --name research --dry-run
+bm project bisync --name research --dry-run
 ```
 
 **What happens:**
@@ -440,20 +432,20 @@ bm project add work --cloud --local-path ~/work-notes
 bm project add personal --cloud --local-path ~/personal
 
 # Establish baselines
-bm cloud bisync --name research --resync
-bm cloud bisync --name work --resync
-bm cloud bisync --name personal --resync
+bm project bisync --name research --resync
+bm project bisync --name work --resync
+bm project bisync --name personal --resync
 
 # Daily workflow: sync everything
-bm cloud bisync --name research
-bm cloud bisync --name work
-bm cloud bisync --name personal
+bm project bisync --name research
+bm project bisync --name work
+bm project bisync --name personal
 ```
 
 **Future:** `--all` flag will sync all configured projects:
 
 ```bash
-bm cloud bisync --all  # Coming soon
+bm project bisync --all  # Coming soon
 ```
 
 ### Mixed Usage
@@ -470,8 +462,8 @@ bm project add archive --cloud
 bm project add temp-notes --cloud
 
 # Sync only the configured ones
-bm cloud bisync --name research
-bm cloud bisync --name work
+bm project bisync --name research
+bm project bisync --name work
 
 # Archive and temp-notes stay cloud-only
 ```
@@ -669,7 +661,7 @@ code ~/.basic-memory/.bmignore
 echo "*.tmp" >> ~/.basic-memory/.bmignore
 
 # Next sync uses updated patterns
-bm cloud bisync --name research
+bm project bisync --name research
 ```
 
 ## Troubleshooting
@@ -732,7 +724,7 @@ bm cloud login
 **Solution:**
 
 ```bash
-bm cloud bisync --name research --resync
+bm project bisync --name research --resync
 ```
 
 **What this does:**
@@ -755,7 +747,7 @@ bm cloud bisync --name research --resync
 echo "# Research Notes" > ~/Documents/research/README.md
 
 # Now run bisync
-bm cloud bisync --name research --resync
+bm project bisync --name research --resync
 ```
 
 **Why this happens:** Bisync creates listing files that track the state of each side. When both directories are completely empty, these listing files are considered invalid by rclone.
@@ -772,10 +764,10 @@ bm cloud bisync --name research --resync
 
 ```bash
 # Clear bisync state
-bm cloud bisync-reset research
+bm project bisync-reset research
 
 # Re-establish baseline
-bm cloud bisync --name research --resync
+bm project bisync --name research --resync
 ```
 
 **What this does:**
@@ -795,16 +787,16 @@ bm cloud bisync --name research --resync
 
 ```bash
 # Check what would be deleted
-bm cloud bisync --name research --dry-run
+bm project bisync --name research --dry-run
 
 # If correct, establish new baseline
-bm cloud bisync --name research --resync
+bm project bisync --name research --resync
 ```
 
 **Solution 2:** Use one-way sync if you know local is correct:
 
 ```bash
-bm cloud sync --name research
+bm project sync --name research
 ```
 
 ### Project Not Configured for Sync
@@ -817,7 +809,7 @@ bm cloud sync --name research
 
 ```bash
 bm cloud sync-setup research ~/Documents/research
-bm cloud bisync --name research --resync
+bm project bisync --name research --resync
 ```
 
 ### Connection Issues
@@ -889,19 +881,19 @@ bm project set-local <name>  # Revert project to local mode
 
 ```bash
 # One-way sync (local → cloud)
-bm cloud sync --name <project>
-bm cloud sync --name <project> --dry-run
-bm cloud sync --name <project> --verbose
+bm project sync --name <project>
+bm project sync --name <project> --dry-run
+bm project sync --name <project> --verbose
 
 # Two-way sync (local ↔ cloud) - Recommended
-bm cloud bisync --name <project>          # After first --resync
-bm cloud bisync --name <project> --resync # First time / force baseline
-bm cloud bisync --name <project> --dry-run
-bm cloud bisync --name <project> --verbose
+bm project bisync --name <project>          # After first --resync
+bm project bisync --name <project> --resync # First time / force baseline
+bm project bisync --name <project> --dry-run
+bm project bisync --name <project> --verbose
 
 # Integrity check
-bm cloud check --name <project>
-bm cloud check --name <project> --one-way
+bm project check --name <project>
+bm project check --name <project> --one-way
 
 # List project files by route
 bm project ls --name <project>          # Default target: local
@@ -917,9 +909,9 @@ bm project ls --name <project> --cloud --path <subpath>
 1. **Authenticate cloud access** - `bm cloud login`
 2. **Install rclone** - `bm cloud setup`
 3. **Add projects with sync** - `bm project add research --cloud --local-path ~/Documents/research`
-4. **Preview first sync** - `bm cloud bisync --name research --resync --dry-run`
-5. **Establish baseline** - `bm cloud bisync --name research --resync`
-6. **Daily workflow** - `bm cloud bisync --name research`
+4. **Preview first sync** - `bm project bisync --name research --resync --dry-run`
+5. **Establish baseline** - `bm project bisync --name research --resync`
+6. **Daily workflow** - `bm project bisync --name research`
 
 **Key benefits:**
 - ✅ Each project independently syncs (or doesn't)

src/basic_memory/cli/commands/cloud/project_sync.py

@@ -95,10 +95,7 @@ def sync_project_command(
     dry_run: bool = typer.Option(False, "--dry-run", help="Preview changes without syncing"),
     verbose: bool = typer.Option(False, "--verbose", "-v", help="Show detailed output"),
 ) -> None:
-    """Personal workspace local mirror only.
-
-    One-way sync: local -> cloud (make cloud identical to local).
-    Not supported for Team workspaces - use cloud API/MCP routing instead.
+    """One-way sync: local -> cloud (make cloud identical to local).
 
     Example:
       bm cloud sync --name research
@@ -146,10 +143,7 @@ def bisync_project_command(
     resync: bool = typer.Option(False, "--resync", help="Force new baseline"),
     verbose: bool = typer.Option(False, "--verbose", "-v", help="Show detailed output"),
 ) -> None:
-    """Personal workspace local mirror only.
-
-    Two-way sync: local <-> cloud (bidirectional sync).
-    Not supported for Team workspaces - use cloud API/MCP routing instead.
+    """Two-way sync: local <-> cloud (bidirectional sync).
 
     Examples:
       bm cloud bisync --name research --resync  # First time
@@ -209,10 +203,7 @@ def check_project_command(
     name: str = typer.Option(..., "--name", help="Project name to check"),
     one_way: bool = typer.Option(False, "--one-way", help="Check one direction only (faster)"),
 ) -> None:
-    """Personal workspace local mirror only.
-
-    Verify file integrity between local and cloud.
-    Not supported for Team workspaces - use cloud API/MCP routing instead.
+    """Verify file integrity between local and cloud.
 
     Example:
       bm cloud check --name research
@@ -255,10 +246,7 @@ def check_project_command(
 def bisync_reset(
     name: str = typer.Argument(..., help="Project name to reset bisync state for"),
 ) -> None:
-    """Personal workspace local mirror only.
-
-    Clear bisync state for a project.
-    Not supported for Team workspaces - use cloud API/MCP routing instead.
+    """Clear bisync state for a project.
 
     This removes the bisync metadata files, forcing a fresh --resync on next bisync.
     Useful when bisync gets into an inconsistent state or when remote path changes.
@@ -289,10 +277,7 @@ def setup_project_sync(
     name: str = typer.Argument(..., help="Project name"),
     local_path: str = typer.Argument(..., help="Local sync directory"),
 ) -> None:
-    """Personal workspace local mirror only.
-
-    Configure local sync for an existing cloud project.
-    Not supported for Team workspaces - use cloud API/MCP routing instead.
+    """Configure local sync for an existing cloud project.
 
     Example:
       bm cloud sync-setup research ~/Documents/research

src/basic_memory/mcp/tools/write_note.py

@@ -1,6 +1,7 @@
 """Write note tool for Basic Memory MCP server."""
 
 import textwrap
+from pathlib import Path
 from typing import Annotated, List, Union, Optional, Literal
 
 import logfire
@@ -269,7 +270,19 @@ async def write_note(
                             raise ValueError(
                                 "Entity permalink is required for updates"
                             )  # pragma: no cover
-                        entity_id = await knowledge_client.resolve_entity(entity.permalink)
+                        # Resolve the conflicting entity by file_path with strict=True.
+                        # The 409 came from a file_service.exists(file_path) check, so this
+                        # file_path is the authoritative key for the canonical row. Resolving
+                        # by permalink with fuzzy fallback (the previous behavior) could pick
+                        # an orphan with a similar permalink — especially in workspace-prefixed
+                        # palaces where the client-built permalink omits the workspace slug —
+                        # causing the update to write to the wrong row and the next call to
+                        # mint a -1/-2 suffix on the canonical entity.
+                        # POSIX-normalize so Windows clients send the same form the server stores.
+                        file_path_identifier = Path(entity.file_path).as_posix()
+                        entity_id = await knowledge_client.resolve_entity(
+                            file_path_identifier, strict=True
+                        )
                         result = await knowledge_client.update_entity(
                             entity_id, entity.model_dump()
                         )

test-int/mcp/test_write_note_integration.py

@@ -5,14 +5,25 @@ Comprehensive tests covering all scenarios including note creation, content form
 tag handling, error conditions, and edge cases from bug reports.
 """
 
+import json
+from pathlib import Path
 from textwrap import dedent
+from typing import Any
 
 import pytest
 from fastmcp import Client
 
 from basic_memory.config import ConfigManager
 from basic_memory.schemas.project_info import ProjectItem
-from pathlib import Path
+
+
+def _json_content(tool_result) -> dict[str, Any]:
+    """Parse a FastMCP tool result content block into a JSON object."""
+    assert len(tool_result.content) == 1
+    assert tool_result.content[0].type == "text"
+    payload = json.loads(tool_result.content[0].text)  # pyright: ignore [reportAttributeAccessIssue]
+    assert isinstance(payload, dict)
+    return payload
 
 
 @pytest.mark.asyncio
@@ -113,6 +124,83 @@ async def test_write_note_update_existing(mcp_server, app, test_project):
         assert f"[Session: Using project '{test_project.name}']" in response_text
 
 
+@pytest.mark.asyncio
+async def test_write_note_overwrite_resolves_conflict_by_file_path_when_permalink_changes(
+    mcp_server, app, test_project, monkeypatch
+):
+    """Overwrite resolves the conflict by strict file path through the MCP client stack."""
+    from basic_memory.mcp.clients import knowledge as knowledge_mod
+
+    original_resolve = knowledge_mod.KnowledgeClient.resolve_entity
+    captured_resolve: dict[str, Any] = {}
+
+    async def spy_resolve(self, identifier: str, *, strict: bool = False) -> str:
+        captured_resolve["identifier"] = identifier
+        captured_resolve["strict"] = strict
+        return await original_resolve(self, identifier, strict=strict)
+
+    monkeypatch.setattr(knowledge_mod.KnowledgeClient, "resolve_entity", spy_resolve)
+
+    async with Client(mcp_server) as client:
+        created = await client.call_tool(
+            "write_note",
+            {
+                "project": test_project.name,
+                "title": "Overwrite Permalink Change",
+                "directory": "overwrite-conflicts",
+                "content": "# Overwrite Permalink Change\n\nOriginal body.",
+                "output_format": "json",
+            },
+        )
+        created_payload = _json_content(created)
+        assert created_payload["permalink"] == (
+            f"{test_project.name}/overwrite-conflicts/overwrite-permalink-change"
+        )
+
+        replacement = dedent("""
+            ---
+            permalink: overwrite-conflicts/custom-overwrite-permalink
+            ---
+
+            # Overwrite Permalink Change
+
+            Replacement body.
+        """).strip()
+
+        updated = await client.call_tool(
+            "write_note",
+            {
+                "project": test_project.name,
+                "title": "Overwrite Permalink Change",
+                "directory": "overwrite-conflicts",
+                "content": replacement,
+                "overwrite": True,
+                "output_format": "json",
+            },
+        )
+        updated_payload = _json_content(updated)
+        assert updated_payload["action"] == "updated"
+        assert updated_payload["permalink"] == "overwrite-conflicts/custom-overwrite-permalink"
+        assert updated_payload["file_path"] == "overwrite-conflicts/Overwrite Permalink Change.md"
+        assert captured_resolve == {
+            "identifier": "overwrite-conflicts/Overwrite Permalink Change.md",
+            "strict": True,
+        }
+
+        read_updated = await client.call_tool(
+            "read_note",
+            {
+                "project": test_project.name,
+                "identifier": "overwrite-conflicts/custom-overwrite-permalink",
+                "output_format": "json",
+            },
+        )
+        read_payload = _json_content(read_updated)
+        assert read_payload["permalink"] == "overwrite-conflicts/custom-overwrite-permalink"
+        assert "Replacement body." in read_payload["content"]
+        assert "Original body." not in read_payload["content"]
+
+
 @pytest.mark.asyncio
 async def test_write_note_tag_array(mcp_server, app, test_project):
     """Test creating a note with tag array (Issue #38 regression test)."""

tests/cli/cloud/test_project_sync_command.py

@@ -12,21 +12,6 @@ from basic_memory.config import ProjectMode
 runner = CliRunner()
 
 
-@pytest.mark.parametrize(
-    "command",
-    ["sync", "bisync", "check", "bisync-reset", "sync-setup"],
-)
-def test_cloud_sync_command_help_marks_personal_workspace_only(command):
-    """Cloud sync help should explain that local mirrors are Personal-only."""
-    importlib.import_module("basic_memory.cli.commands.cloud.project_sync")
-
-    result = runner.invoke(app, ["cloud", command, "--help"])
-
-    assert result.exit_code == 0, result.output
-    assert "Personal workspace local mirror only" in result.output
-    assert "Not supported for Team workspaces" in result.output
-
-
 @pytest.mark.parametrize(
     "argv",
     [

tests/mcp/test_tool_write_note.py

@@ -1311,3 +1311,76 @@ class TestWriteNoteOverwriteGuard:
         assert "# Created note" in result
         assert f"project: {test_project.name}" in result
         assert "file_path: guard/Brand New Note.md" in result
+
+    @pytest.mark.asyncio
+    async def test_write_note_overwrite_resolves_by_file_path_strictly(
+        self, app, test_project, entity_repository, monkeypatch
+    ):
+        """Regression: overwrite=True must resolve the conflicting entity by
+        file_path with strict=True, not by permalink with fuzzy fallback.
+
+        Bug shape: in workspace-prefixed palaces the client-built permalink
+        omits the workspace slug, so resolve_entity(permalink) with the default
+        strict=False would fall through to fuzzy search and could pick an
+        orphan row sharing tokens with the canonical permalink. The update
+        then wrote to the orphan, the canonical row stayed stale, and the
+        next overwrite minted a -1/-2 suffix because the permalink uniqueness
+        check found duplicate rows.
+
+        The 409 we catch came from a file_service.exists(file_path) check,
+        so file_path is the authoritative key — strict resolution against it
+        is safe even when permalinks are workspace-prefixed elsewhere.
+        """
+        # Spy on the resolve_entity call to assert the identifier and strict flag.
+        from basic_memory.mcp.clients import knowledge as knowledge_mod
+
+        original_resolve = knowledge_mod.KnowledgeClient.resolve_entity
+        captured: dict[str, Any] = {}
+
+        async def spy_resolve(self, identifier, *, strict=False):
+            captured["identifier"] = identifier
+            captured["strict"] = strict
+            return await original_resolve(self, identifier, strict=strict)
+
+        monkeypatch.setattr(knowledge_mod.KnowledgeClient, "resolve_entity", spy_resolve)
+
+        # Create then overwrite the canonical note.
+        await write_note(
+            project=test_project.name,
+            title="Overview",
+            directory="features/foo",
+            content="# Overview\n\nVersion A",
+        )
+        canonical_permalink = f"{test_project.name}/features/foo/overview"
+        canonical = await entity_repository.get_by_permalink(canonical_permalink)
+        assert canonical is not None
+        canonical_id = canonical.id
+
+        result = await write_note(
+            project=test_project.name,
+            title="Overview",
+            directory="features/foo",
+            content="# Overview\n\nVersion B",
+            overwrite=True,
+        )
+        assert "# Updated note" in result
+
+        # The overwrite path resolved by file_path with strict=True — not by
+        # permalink with the default fuzzy fallback.
+        assert captured.get("identifier") == "features/foo/Overview.md"
+        assert captured.get("strict") is True
+
+        # And the canonical row was updated in place — no duplicate -1/-2 row.
+        canonical_after = await entity_repository.get_by_permalink(canonical_permalink)
+        assert canonical_after is not None
+        assert canonical_after.id == canonical_id
+
+        content = await read_note(canonical_permalink, project=test_project.name)
+        assert "Version B" in content
+        assert "Version A" not in content
+
+        for suffix in ("-1", "-2"):
+            stray = await entity_repository.get_by_permalink(f"{canonical_permalink}{suffix}")
+            assert stray is None, (
+                f"overwrite=True minted a stray '{suffix}' suffix on the canonical permalink"
+            )