v3.0.1: refactor(core): Refine processor, db, and command handling

Refactor processor initialization to remove redundant channel passing in src/cmd/serve.rs.
Refactor the processor tick loop to use tokio::select for shutdown and tick handling in src/cmd/serve.rs.
Removed duplicated pragmas from database initialization and consolidated to migration in src/data/repository.rs.
Added a trace log before closing the read pool in src/data/repository.rs.
Modified the cleanup to close write pool only when no other references exist in src/data/repository.rs.
Adjusted the cleanup process to remove WAL/SHM files during cleanup in src/data/repository.rs.
Corrected a typo from 'jounal_mode' to 'journal_mode' in the repository lock/unlock procedures in src/data/repository.rs.
Modified write lock to execute `PRAGMA wal_checkpoint(TRUNCATE)` in src/data/repository.rs.
Modified write unlock to execute `PRAGMA wal_checkpoint(PASSIVE)` in src/data/repository.rs.
Renamed 'handler' module to 'command_handler' in src/files/mod.rs.
Updated log message in shutdown handler for file processing to be command handling in src/files/command_handler.rs.
Removed redundant clone from processor initialization in src/files/processor.rs.
Updated log message in shutdown handler for api server in src/server/api.rs.