Add MCP server functions for repair commands (bd-7bbc4e6a)

- Add repair_deps(fix=False) for orphaned dependencies
- Add detect_pollution(clean=False) for test issue detection
- Add validate(checks=None, fix_all=False) for health checks
- Implemented in BdCliClient, stubs in BdDaemonClient
- Registered as MCP tools in server.py

Amp-Thread-ID: https://ampcode.com/threads/T-9ce04c75-201b-4019-b9f1-0cf10663557c
Co-authored-by: Amp <amp@ampcode.com>

integrations/beads-mcp/src/beads_mcp/bd_client.py

@@ -139,6 +139,43 @@ class BdClientBase(ABC):
         """Get current database schema for inspection."""
         pass
 
+    @abstractmethod
+    async def repair_deps(self, fix: bool = False) -> dict:
+        """Find and optionally fix orphaned dependency references.
+        
+        Args:
+            fix: If True, automatically remove orphaned dependencies
+            
+        Returns:
+            Dict with orphans_found, orphans list, and fixed count if fix=True
+        """
+        pass
+
+    @abstractmethod
+    async def detect_pollution(self, clean: bool = False) -> dict:
+        """Detect test issues that leaked into production database.
+        
+        Args:
+            clean: If True, delete detected test issues
+            
+        Returns:
+            Dict with detected test issues and deleted count if clean=True
+        """
+        pass
+
+    @abstractmethod
+    async def validate(self, checks: str | None = None, fix_all: bool = False) -> dict:
+        """Run database validation checks.
+        
+        Args:
+            checks: Comma-separated list of checks (orphans,duplicates,pollution,conflicts)
+            fix_all: If True, auto-fix all fixable issues
+            
+        Returns:
+            Dict with validation results for each check
+        """
+        pass
+
 
 class BdCliClient(BdClientBase):
     """Client for calling bd CLI commands and parsing JSON output."""
@@ -623,6 +660,63 @@ class BdCliClient(BdClientBase):
             raise BdCommandError("Invalid response for get_schema_info")
         return data
 
+    async def repair_deps(self, fix: bool = False) -> dict:
+        """Find and optionally fix orphaned dependency references.
+
+        Args:
+            fix: If True, automatically remove orphaned dependencies
+
+        Returns:
+            Dict with orphans_found, orphans list, and fixed count if fix=True
+        """
+        args = ["repair-deps"]
+        if fix:
+            args.append("--fix")
+
+        data = await self._run_command(*args)
+        if not isinstance(data, dict):
+            raise BdCommandError("Invalid response for repair-deps")
+        return data
+
+    async def detect_pollution(self, clean: bool = False) -> dict:
+        """Detect test issues that leaked into production database.
+
+        Args:
+            clean: If True, delete detected test issues
+
+        Returns:
+            Dict with detected test issues and deleted count if clean=True
+        """
+        args = ["detect-pollution"]
+        if clean:
+            args.extend(["--clean", "--yes"])
+
+        data = await self._run_command(*args)
+        if not isinstance(data, dict):
+            raise BdCommandError("Invalid response for detect-pollution")
+        return data
+
+    async def validate(self, checks: str | None = None, fix_all: bool = False) -> dict:
+        """Run database validation checks.
+
+        Args:
+            checks: Comma-separated list of checks (orphans,duplicates,pollution,conflicts)
+            fix_all: If True, auto-fix all fixable issues
+
+        Returns:
+            Dict with validation results for each check
+        """
+        args = ["validate"]
+        if checks:
+            args.extend(["--checks", checks])
+        if fix_all:
+            args.append("--fix-all")
+
+        data = await self._run_command(*args)
+        if not isinstance(data, dict):
+            raise BdCommandError("Invalid response for validate")
+        return data
+
     async def init(self, params: InitParams | None = None) -> str:
         """Initialize bd in current directory.
 

integrations/beads-mcp/src/beads_mcp/bd_daemon_client.py

@@ -452,6 +452,49 @@ class BdDaemonClient(BdClientBase):
         """
         raise NotImplementedError("get_schema_info not supported via daemon - use CLI client")
 
+    async def repair_deps(self, fix: bool = False) -> dict:
+        """Find and optionally fix orphaned dependency references.
+
+        Args:
+            fix: If True, automatically remove orphaned dependencies
+
+        Returns:
+            Dict with orphans_found, orphans list, and fixed count if fix=True
+
+        Note:
+            This falls back to CLI since repair operations are rare
+        """
+        raise NotImplementedError("repair_deps not supported via daemon - use CLI client")
+
+    async def detect_pollution(self, clean: bool = False) -> dict:
+        """Detect test issues that leaked into production database.
+
+        Args:
+            clean: If True, delete detected test issues
+
+        Returns:
+            Dict with detected test issues and deleted count if clean=True
+
+        Note:
+            This falls back to CLI since pollution detection is a rare operation
+        """
+        raise NotImplementedError("detect_pollution not supported via daemon - use CLI client")
+
+    async def validate(self, checks: str | None = None, fix_all: bool = False) -> dict:
+        """Run database validation checks.
+
+        Args:
+            checks: Comma-separated list of checks (orphans,duplicates,pollution,conflicts)
+            fix_all: If True, auto-fix all fixable issues
+
+        Returns:
+            Dict with validation results for each check
+
+        Note:
+            This falls back to CLI since validation is a rare operation
+        """
+        raise NotImplementedError("validate not supported via daemon - use CLI client")
+
     async def add_dependency(self, params: AddDependencyParams) -> None:
         """Add a dependency between issues.
 

integrations/beads-mcp/src/beads_mcp/server.py

@@ -19,16 +19,19 @@ from beads_mcp.tools import (
     beads_blocked,
     beads_close_issue,
     beads_create_issue,
+    beads_detect_pollution,
     beads_get_schema_info,
     beads_init,
     beads_inspect_migration,
     beads_list_issues,
     beads_quickstart,
     beads_ready_work,
+    beads_repair_deps,
     beads_reopen_issue,
     beads_show_issue,
     beads_stats,
     beads_update_issue,
+    beads_validate,
     current_workspace,  # ContextVar for per-request workspace routing
 )
 
@@ -602,6 +605,53 @@ async def get_schema_info(workspace_root: str | None = None) -> dict:
     return await beads_get_schema_info()
 
 
+@mcp.tool(
+    name="repair_deps",
+    description="Find and optionally fix orphaned dependency references.",
+)
+@with_workspace
+async def repair_deps(fix: bool = False, workspace_root: str | None = None) -> dict:
+    """Find and optionally fix orphaned dependency references.
+    
+    Scans all issues for dependencies pointing to non-existent issues.
+    Returns orphaned dependencies and optionally removes them with fix=True.
+    """
+    return await beads_repair_deps(fix=fix)
+
+
+@mcp.tool(
+    name="detect_pollution",
+    description="Detect test issues that leaked into production database.",
+)
+@with_workspace
+async def detect_pollution(clean: bool = False, workspace_root: str | None = None) -> dict:
+    """Detect test issues that leaked into production database.
+    
+    Detects test issues using pattern matching (titles starting with 'test', etc.).
+    Returns detected test issues and optionally deletes them with clean=True.
+    """
+    return await beads_detect_pollution(clean=clean)
+
+
+@mcp.tool(
+    name="validate",
+    description="Run comprehensive database health checks.",
+)
+@with_workspace
+async def validate(
+    checks: str | None = None,
+    fix_all: bool = False,
+    workspace_root: str | None = None,
+) -> dict:
+    """Run comprehensive database health checks.
+    
+    Available checks: orphans, duplicates, pollution, conflicts.
+    If checks is None, runs all checks.
+    Returns validation results for each check.
+    """
+    return await beads_validate(checks=checks, fix_all=fix_all)
+
+
 async def async_main() -> None:
     """Async entry point for the MCP server."""
     await mcp.run_async(transport="stdio")

integrations/beads-mcp/src/beads_mcp/tools.py

@@ -484,6 +484,60 @@ async def beads_get_schema_info() -> dict:
     return await client.get_schema_info()
 
 
+async def beads_repair_deps(
+    fix: Annotated[bool, "If True, automatically remove orphaned dependencies"] = False,
+) -> dict:
+    """Find and optionally fix orphaned dependency references.
+    
+    Scans all issues for dependencies pointing to non-existent issues.
+    Returns orphaned dependencies and optionally removes them with fix=True.
+    
+    Returns dict with:
+    - orphans_found: number of orphaned dependencies
+    - orphans: list of orphaned dependency details
+    - fixed: number of orphans fixed (if fix=True)
+    """
+    client = await _get_client()
+    return await client.repair_deps(fix=fix)
+
+
+async def beads_detect_pollution(
+    clean: Annotated[bool, "If True, delete detected test issues"] = False,
+) -> dict:
+    """Detect test issues that leaked into production database.
+    
+    Detects test issues using pattern matching:
+    - Titles starting with 'test', 'benchmark', 'sample', 'tmp', 'temp'
+    - Sequential numbering (test-1, test-2, ...)
+    - Generic descriptions or no description
+    - Created in rapid succession
+    
+    Returns dict with detected test issues and deleted count if clean=True.
+    """
+    client = await _get_client()
+    return await client.detect_pollution(clean=clean)
+
+
+async def beads_validate(
+    checks: Annotated[str | None, "Comma-separated list of checks (orphans,duplicates,pollution,conflicts)"] = None,
+    fix_all: Annotated[bool, "If True, auto-fix all fixable issues"] = False,
+) -> dict:
+    """Run comprehensive database health checks.
+    
+    Available checks:
+    - orphans: Orphaned dependencies (references to deleted issues)
+    - duplicates: Duplicate issues (identical content)
+    - pollution: Test pollution (leaked test issues)
+    - conflicts: Git merge conflicts in JSONL
+    
+    If checks is None, runs all checks.
+    
+    Returns dict with validation results for each check.
+    """
+    client = await _get_client()
+    return await client.validate(checks=checks, fix_all=fix_all)
+
+
 async def beads_init(
     prefix: Annotated[str | None, "Issue prefix (e.g., 'myproject' for myproject-1, myproject-2)"] = None,
 ) -> str: