feat: Implement persistent agent state management and process handling

[doroteaMonaco]

• Added PersistentAgentRegistry for managing agent metadata on disk.
• Introduced AgentProcessManager for spawning and managing agent processes.
• Updated agent commands (start, stop, list) to utilize persistent storage.
• Enhanced agent metadata structure to include process tracking and state management.
• Implemented configuration validation for agent startup.
• Refactored CLI context to include persistent agent registry and process manager.
• Added timestamp formatting for agent start/stop events.

📋 Summary

This PR introduces the PersistentAgentRegistry and AgentProcessManager subsystems, enabling the CLI to manage agent processes with full lifecycle tracking, persistent state, and cross-platform compatibility. Agent commands now operate on real data stored in ~/.local/share/mofa/agents/ instead of returning hardcoded responses.

🔗 Related Issues

Closes #

Related to #127

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🧠 Context

Problem: The agent CLI commands (list, start, stop) were returning hardcoded stub responses without actually managing processes or persisting state.

Solution:

• New PersistentAgentRegistry saves agent metadata to disk in JSON format
• New AgentProcessManager spawns/terminates agent processes and tracks PIDs
• Agent commands updated to read/write persistent state and manage real processes
• Configuration validation ensures only valid agents can be started

Design Decisions:

• Using JSON format for persistence (human-readable, easy backup/restore)
• Cross-platform process management (Unix signals + Windows TerminateProcess)
• Metadata tracks: PID, state, timestamps, start count for debugging

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🛠️ Changes

• Added PersistentAgentRegistry (src/state/agent_state.rs) - Manages agent metadata lifecycle with disk persistence
• Added AgentProcessManager (src/utils/process_manager.rs) - Spawns/terminates processes with platform-specific signals
• Updated agent start command - Validates config, creates process, records metadata
• Updated agent stop command - Sends SIGTERM/TerminateProcess and updates state
• Updated agent list command - Reads from disk and displays running/stopped agents with timestamps
• Enhanced AgentMetadata structure - Added PID, state, timestamps, start count
• Updated CLI context - Injected PersistentAgentRegistry and AgentProcessManager
• Added helper: format_timestamp() for human-readable time display (src/commands/agent/list.rs)

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🧪 How you Tested

Unit Tests (27 total, all passing):

1. Created test_agent_metadata_lifecycle - Verifies state transitions (Stopped → Running → Stopped)
2. Created test_registry_persistence - Ensures agent data survives disk I/O
3. Created test_list_running_agents - Confirms filtering logic works
4. Created test_process_manager_creation - Validates PM initialization
5. Created test_validate_config_missing_file - Error handling for missing config
6. Created test_validate_config_valid_yaml - Accepts valid YAML config
7. Created test_validate_config_invalid_yaml - Rejects malformed config

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📸 Screenshots / Logs (if applicable)

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⚠️ Breaking Changes

• [X ] No breaking changes
• Breaking change (describe below)

If breaking:

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🧹 Checklist

Code Quality

• [X ] Code follows Rust idioms and project conventions
• [X ] cargo fmt run
• [ X] cargo clippy passes without warnings

Testing

• [X ] Tests added/updated
• [ X] cargo test passes locally without any error

Documentation

• Public APIs documented
• README / docs updated (if needed)

PR Hygiene

• [ X] PR is small and focused (one logical change)
• [X ] Branch is up to date with main
• [X ] No unrelated commits
• [X ] Commit messages explain why, not only what

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🚀 Deployment Notes (if applicable)

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🧩 Additional Notes for Reviewers

[lijingrs]

The code on your branch is not up to date. Please sync and merge the latest code from the main branch.

[doroteaMonaco]

Done, thanks!

[lijingrs]

There are code conflicts. Could you please sync and pull the latest code, then merge it into your current branch in your IDE?