Add bulk operations and remove collections abstraction

- Add bulk delete, bulk tags, and bulk set-tags engine endpoints
  (POST /api/v1/bulk/delete, /bulk/tags, /bulk/set-tags)
- Filter-based selection: by tags, doc_type, ID list, ID range
- Safety threshold (KB_BULK_SAFETY_PERCENT, default 70%) prevents
  accidental mass operations unless force=true
- Synchronous execution with audit trail via jobs table
- Add kb_bulk_delete, kb_bulk_tags, kb_bulk_set_tags MCP tools
- Add kb bulk-remove, bulk-tag, bulk-set-tags CLI commands
- Remove collection abstraction from MCP server (use tags instead)
- Remove kb_set_collection MCP tool
- Update SKILL.md, MCP.md, README.md documentation

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

engine/main.py

@@ -62,7 +62,7 @@ async def lifespan(app: FastAPI):
 app = FastAPI(title="kb-engine", version=__version__, lifespan=lifespan)
 
 # Import routes after app is created
-from kb.routes import health, search, jobs, documents, tags, status, reindex, auth, notes  # noqa: E402, F401
+from kb.routes import health, search, jobs, documents, tags, status, reindex, auth, notes, bulk  # noqa: E402, F401
 
 if __name__ == "__main__":
     import uvicorn