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_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.