Add flag to optimize db. Remove ANALYZE on startup.

Entire-Checkpoint: d49917ff4b10

internal/repository/dbConnection.go

@@ -49,14 +49,6 @@ func setupSqlite(db *sql.DB, cfg *RepositoryConfig) error {
 		}
 	}
 
-	// Update query planner statistics so SQLite picks optimal indexes.
-	// Without this, SQLite guesses row distributions and often chooses wrong
-	// indexes for queries with IN clauses + ORDER BY, causing full table sorts
-	// in temp B-trees instead of using covering indexes.
-	if _, err := db.Exec("ANALYZE"); err != nil {
-		cclog.Warnf("Failed to run ANALYZE: %v", err)
-	}
-
 	return nil
 }