Feat/cs/refactor shutdown

[ReagentX]

• Refactor shutdown process
  • Use AtomicBool instead of Mutex<bool>
  • Store thread handles and child processes in a InputStream
  • Fix Command streams with no output do not terminate correctly #132
• Fix unassigned stream handles if saving the session file failed, but the app started anyway

[Copilot]

Pull Request Overview

This PR refactors the shutdown process and modifies how streams are managed during application exit. Key changes include:

• Replacing Mutex with AtomicBool for shutdown signaling and adjusting thread handling in shutdown.
• Storing thread handles and child process references in InputStream and updating error handling.
• Improving startup error recovery to prevent unassigned stream handles.

Reviewed Changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated no comments.

File	Description
src/util/error.rs	Updated error message for invalid commands.
src/communication/reader.rs	Changed shutdown logic to use AtomicBool, join threads, and update shutdown procedure.
src/communication/input.rs	Refactored CommandInput to use AtomicBool and store thread handles and child processes.
src/communication/handlers/startup.rs	Enhanced error handling by matching on build_streams_from_input result.