feat: Fix bm CLI runtime defects and audit regressions

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

@@ -52,7 +52,7 @@ async def get_authenticated_headers(auth: CLIAuth | None = None) -> dict[str, st
     auth_obj = auth or CLIAuth(client_id=client_id, authkit_domain=domain)
     token = await auth_obj.get_valid_token()
     if not token:
-        console.print("[red]Not authenticated. Please run 'basic-memory cloud login' first.[/red]")
+        console.print("[red]Not authenticated. Please run 'bm cloud login' first.[/red]")
         raise typer.Exit(1)
 
     return {"Authorization": f"Bearer {token}"}

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

@@ -151,7 +151,7 @@ def setup() -> None:
     """Set up cloud sync by installing rclone and configuring credentials.
 
     After setup, use project commands for syncing:
-      bm project add <name> <path> --local-path ~/projects/<name>
+      bm project add <name> --cloud --local-path ~/projects/<name>
       bm project bisync --name <name> --resync  # First time
       bm project bisync --name <name>            # Subsequent syncs
     """
@@ -183,7 +183,7 @@ def setup() -> None:
         console.print("\n[bold green]Cloud setup completed successfully![/bold green]")
         console.print("\n[bold]Next steps:[/bold]")
         console.print("1. Add a project with local sync path:")
-        console.print("   bm project add research --local-path ~/Documents/research")
+        console.print("   bm project add research --cloud --local-path ~/Documents/research")
         console.print("\n   Or configure sync for an existing project:")
         console.print("   bm project sync-setup research ~/Documents/research")
         console.print("\n2. Preview the initial sync (recommended):")

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

@@ -13,6 +13,7 @@
     sync_project,
 )
 from basic_memory.cli.commands.cloud.upload import upload_path
+from basic_memory.mcp.async_client import get_cloud_control_plane_client
 
 console = Console()
 
@@ -86,7 +87,7 @@ async def _upload():
                 console.print(
                     f"[red]Project '{project}' does not exist.[/red]\n"
                     f"[yellow]Options:[/yellow]\n"
-                    f"  1. Create it first: bm project add {project}\n"
+                    f"  1. Create it first: bm project add {project} --cloud\n"
                     f"  2. Use --create-project flag to create automatically"
                 )
                 raise typer.Exit(1)
@@ -100,7 +101,12 @@ async def _upload():
             console.print(f"[blue]Uploading {path} to project '{project}'...[/blue]")
 
         success = await upload_path(
-            path, project, verbose=verbose, use_gitignore=not no_gitignore, dry_run=dry_run
+            path,
+            project,
+            verbose=verbose,
+            use_gitignore=not no_gitignore,
+            dry_run=dry_run,
+            client_cm_factory=get_cloud_control_plane_client,
         )
         if not success:
             console.print("[red]Upload failed[/red]")

src/basic_memory/cli/commands/command_utils.py

@@ -97,5 +97,19 @@ async def get_project_info(project: str):
             response = await call_get(client, f"/v2/projects/{project_item.external_id}/info")
             return ProjectInfoResponse.model_validate(response.json())
     except (ToolError, ValueError) as e:
-        console.print(f"[red]Sync failed: {e}[/red]")
+        error_text = str(e)
+        if "internal proxy error" in error_text.lower() and "not found in configuration" in (
+            error_text.lower()
+        ):
+            console.print(
+                "[red]Project info failed: cloud returned an internal configuration error for "
+                "this project.[/red]"
+            )
+            console.print(
+                "[yellow]This is a cloud backend issue for detailed info lookups. "
+                "Use `bm project list --cloud` for project metadata until the service is updated."
+                "[/yellow]"
+            )
+        else:
+            console.print(f"[red]Project info failed: {e}[/red]")
         raise typer.Exit(1)

src/basic_memory/cli/commands/format.py

@@ -183,10 +183,10 @@ def format(
     By default, formats all .md, .json, and .canvas files in the current project.
 
     Examples:
-        basic-memory format                    # Format all files in current project
-        basic-memory format --project research # Format files in specific project
-        basic-memory format notes/meeting.md   # Format a specific file
-        basic-memory format notes/             # Format all files in directory
+        bm format                    # Format all files in current project
+        bm format --project research # Format files in specific project
+        bm format notes/meeting.md   # Format a specific file
+        bm format notes/             # Format all files in directory
     """
     try:
         run_with_cleanup(run_format(path, project))

src/basic_memory/cli/commands/import_chatgpt.py

@@ -44,7 +44,7 @@ def import_chatgpt(
     2. Convert them to linear markdown conversations
     3. Save as clean, readable markdown files
 
-    After importing, run 'basic-memory sync' to index the new files.
+    After importing, run 'bm reindex --search' to index the new files.
     """
 
     try:
@@ -81,7 +81,7 @@ def import_chatgpt(
             )
         )
 
-        console.print("\nRun 'basic-memory sync' to index the new files.")
+        console.print("\nRun 'bm reindex --search' to index the new files.")
 
     except Exception as e:
         logger.error("Import failed")

src/basic_memory/cli/commands/import_claude_conversations.py

@@ -44,7 +44,7 @@ def import_claude(
     2. Create markdown files for each conversation
     3. Format content in clean, readable markdown
 
-    After importing, run 'basic-memory sync' to index the new files.
+    After importing, run 'bm reindex --search' to index the new files.
     """
 
     config = get_project_config()
@@ -84,7 +84,7 @@ def import_claude(
             )
         )
 
-        console.print("\nRun 'basic-memory sync' to index the new files.")
+        console.print("\nRun 'bm reindex --search' to index the new files.")
 
     except Exception as e:
         logger.error("Import failed")

src/basic_memory/cli/commands/import_claude_projects.py

@@ -44,7 +44,7 @@ def import_projects(
     2. Store docs in a docs/ subdirectory
     3. Place prompt template in project root
 
-    After importing, run 'basic-memory sync' to index the new files.
+    After importing, run 'bm reindex --search' to index the new files.
     """
     config = get_project_config()
     try:
@@ -83,7 +83,7 @@ def import_projects(
             )
         )
 
-        console.print("\nRun 'basic-memory sync' to index the new files.")
+        console.print("\nRun 'bm reindex --search' to index the new files.")
 
     except Exception as e:
         logger.error("Import failed")

src/basic_memory/cli/commands/mcp.py

@@ -36,7 +36,7 @@ def mcp(
     This command starts an MCP server using one of three transport options:
 
     - stdio: Standard I/O (good for local usage)
-    - streamable-http: Recommended for web deployments (default)
+    - streamable-http: Recommended for web deployments
     - sse: Server-Sent Events (for compatibility with existing clients)
 
     Initialization, file sync, and cleanup are handled by the MCP server's lifespan.

src/basic_memory/cli/commands/project.py

@@ -1149,6 +1149,8 @@ def display_project_info(
             )
             console.print(f"\nTimestamp: [cyan]{current_time.strftime('%Y-%m-%d %H:%M:%S')}[/cyan]")
 
+    except typer.Exit:
+        raise
     except Exception as e:  # pragma: no cover
         typer.echo(f"Error getting project info: {e}", err=True)
         raise typer.Exit(1)

src/basic_memory/cli/commands/tool.py

@@ -298,7 +298,7 @@ def write_note(
     content: Annotated[
         Optional[str],
         typer.Option(
-            help="The content of the note. If not provided, content will be read from stdin. This allows piping content from other commands, e.g.: cat file.md | basic-memory tools write-note"
+            help="The content of the note. If not provided, content will be read from stdin. This allows piping content from other commands, e.g.: cat file.md | bm tool write-note"
         ),
     ] = None,
     tags: Annotated[
@@ -322,13 +322,13 @@ def write_note(
     Examples:
 
     # Using content parameter
-    basic-memory tools write-note --title "My Note" --folder "notes" --content "Note content"
+    bm tool write-note --title "My Note" --folder "notes" --content "Note content"
 
     # Using stdin pipe
-    echo "# My Note Content" | basic-memory tools write-note --title "My Note" --folder "notes"
+    echo "# My Note Content" | bm tool write-note --title "My Note" --folder "notes"
 
     # Using heredoc
-    cat << EOF | basic-memory tools write-note --title "My Note" --folder "notes"
+    cat << EOF | bm tool write-note --title "My Note" --folder "notes"
     # My Document
 
     This is my document content.
@@ -338,10 +338,10 @@ def write_note(
     EOF
 
     # Reading from a file
-    cat document.md | basic-memory tools write-note --title "Document" --folder "docs"
+    cat document.md | bm tool write-note --title "Document" --folder "docs"
 
     # Force local routing in cloud mode
-    basic-memory tools write-note --title "My Note" --folder "notes" --content "..." --local
+    bm tool write-note --title "My Note" --folder "notes" --content "..." --local
     """
     try:
         validate_routing_flags(local, cloud)

src/basic_memory/db.py

@@ -476,21 +476,22 @@ async def run_migrations(
     so it's safe to call this multiple times - it will only run pending migrations.
     """
     logger.info("Running database migrations...")
+    temp_engine: AsyncEngine | None = None
     try:
         revisions_before_upgrade: set[str] = set()
         # Trigger: run_migrations() can be invoked before module-level session maker is set.
         # Why: we still need reliable before/after revision detection for one-time backfill.
         # Outcome: create a short-lived session maker when needed, then dispose it immediately.
         if _session_maker is None:
-            temp_engine, temp_session_maker = _create_engine_and_session(
+            precheck_engine, temp_session_maker = _create_engine_and_session(
                 app_config.database_path,
                 database_type,
                 app_config,
             )
             try:
                 revisions_before_upgrade = await _load_applied_alembic_revisions(temp_session_maker)
             finally:
-                await temp_engine.dispose()
+                await precheck_engine.dispose()
         else:
             revisions_before_upgrade = await _load_applied_alembic_revisions(_session_maker)
 
@@ -517,7 +518,9 @@ async def run_migrations(
 
         # Get session maker - ensure we don't trigger recursive migration calls
         if _session_maker is None:
-            _, session_maker = _create_engine_and_session(app_config.database_path, database_type)
+            temp_engine, session_maker = _create_engine_and_session(
+                app_config.database_path, database_type, app_config
+            )
         else:
             session_maker = _session_maker
 
@@ -542,3 +545,11 @@ async def run_migrations(
     except Exception as e:  # pragma: no cover
         logger.error(f"Error running migrations: {e}")
         raise
+    finally:
+        # Trigger: run_migrations() created a temporary engine while module-level
+        # session maker was not initialized.
+        # Why: temporary aiosqlite worker threads can outlive CLI command execution
+        # and block process shutdown if the engine is not disposed.
+        # Outcome: always dispose temporary engines after migration work completes.
+        if temp_engine is not None:
+            await temp_engine.dispose()

src/basic_memory/mcp/tools/project_management.py

@@ -65,9 +65,7 @@ async def list_memory_projects(
         result = "Available projects:\n"
         for project in project_list.projects:
             label = (
-                f"{project.display_name} ({project.name})"
-                if project.display_name
-                else project.name
+                f"{project.display_name} ({project.name})" if project.display_name else project.name
             )
             result += f"• {label}\n"