feat(cli): wire CLI commands to mofa-kernel/foundation backend (issue #146)

[Copilot]

📋 Summary

All mofa-cli command handlers were empty stubs returning Ok(()). This PR replaces every stub with real backend integration — agent lifecycle through AgentRegistry, sessions through SessionManager, plugins through SimplePluginRegistry, and tools through ToolRegistry — plus file-backed persistence so state survives process restarts.

🔗 Related Issues

Related to mofa-org#146

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🧠 Context

CLI commands called // TODO: Implement and returned immediately. No connection existed to the kernel/foundation service layer. A previous attempt built a parallel JSON-file backend that didn't touch existing registries; this PR wires directly to the established crates instead.

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🛠️ Changes

• store.rs (new) — Generic PersistedStore<T> writing per-item .json files; safe filename sanitization prevents path traversal
• context.rs — CliContext now owns AgentRegistry, SessionManager, SimplePluginRegistry, ToolRegistry, and three PersistedStore instances; registers CliBaseAgentFactory; seeds and replays plugin/tool specs on startup; migrates legacy nested session dirs
• agent/start.rs — create_and_register() via selected factory (--type flag added); atomic: rolls back in-memory registration if persistence fails
• agent/stop.rs — agent.shutdown() → persist "Stopped" → registry.unregister(); restores persisted state if unregister fails
• agent/restart.rs — delegates to stop::run + start::run
• agent/list.rs — merges live registry entries with agent_store so stopped-but-persisted agents appear
• plugin/uninstall.rs — marks spec enabled=false in plugin_store before unregistering; rollback on failure
• session/export.rs, show.rs, list.rs — switched from get_or_create() to new SessionManager::get() that returns Option without side-effects
• mofa-foundation/session.rs — added SessionManager::get(); fixed list() to read canonical key from JSONL header (preserves _ in keys, no more _→: corruption)

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🧪 How you Tested

1. cargo test -p mofa-cli — 37 unit + 4 integration tests, all pass
2. cargo test -p mofa-foundation — 203 tests pass
3. Key scenarios covered by tests: start→stop→restart chain, duplicate-start error, unknown factory type, persist-across-context-instances, disabled plugin not replayed, legacy session migration, session list without phantom creation

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📸 Screenshots / Logs (if applicable)

running 37 tests
test commands::agent::start::tests::test_start_succeeds_with_default_factory ... ok
test commands::agent::stop::tests::test_stop_updates_state_and_unregisters_agent ... ok
test commands::agent::restart::tests::test_restart_chain_start_stop_restart_list ... ok
test context::tests::test_agent_store_persists_across_context_instances ... ok
test context::tests::test_plugin_and_tool_specs_replayed_on_startup ... ok
...
test result: ok. 37 passed; 0 failed

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⚠️ Breaking Changes

• No breaking changes

If breaking:

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🧹 Checklist

Code Quality

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

Testing

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

Documentation

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

PR Hygiene

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

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🚀 Deployment Notes (if applicable)

On first run after upgrade, CliContext::new() creates ~/.local/share/mofa/{agents,plugins,tools}/ directories and seeds default plugin/tool specs. Existing session files under the legacy sessions/sessions/ nesting are migrated automatically.

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🧩 Additional Notes for Reviewers

• PersistedStore sanitizes IDs to [a-zA-Z0-9\-_.] before constructing file paths — no additional validation needed at call sites
• Rollback paths in start/stop/uninstall are best-effort; failure messages distinguish "operation failed" from "rollback also failed"
• SessionManager::get() is the canonical non-mutating lookup — callers that previously used get_or_create() and then checked is_empty() now get a proper None instead

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