fix: critical session lifecycle and permission persistence bugs

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Summary

Automated bug investigation found and fixed several high-severity correctness issues in session management, database persistence, and feed loading.

Bugs fixed

1. Permission bypass after restart (security)

Impact: Sessions created in approval mode silently switched to auto-approve after app restart or follow-up message reload.

Root cause: get_session SELECT omitted skip_permissions, parent_session_id, and depth columns (indices 15–17), causing skip_permissions to always default to true. create_session also never persisted skip_permissions to the DB.

Fix: Align get_session SELECT with get_sessions; persist skip_permissions on INSERT based on permission_mode.

2. Stopped sessions marked completed

Impact: Stopping a running session briefly showed "stopped" then flipped to "completed" when the CLI process exited.

Root cause: reader_loop unconditionally wrote Completed to DB on exit, racing with stop_session.

Fix: reader_exit_status() checks DB status and preserves Stopped.

3. Orphan CLI on session delete

Impact: Deleting a running session left the CLI process running in the background, continuing to emit events and write to DB.

Root cause: delete_session removed in-memory/DB state but never called kill_pid.

Fix: Kill process and clean up PID file before deletion (same as stop_session).

4. Silent JSONL loss on DB lock

Impact: Session chat output could be permanently lost under SQLite lock contention.

Root cause: flush_batch cleared its entire buffer when BEGIN failed.

Fix: Retain buffer for retry on next flush cycle.

5. Live feed wiped on tab switch

Impact: Switching back to an active session could erase messages that arrived while away.

Root cause: loadHistory replaced the in-memory journal array with the (stale) DB snapshot.

Fix: Merge DB history with live entries by seq.

Tests added

• should_persist_skip_permissions_from_permission_mode_on_create
• should_load_parent_and_depth_via_get_session
• should_preserve_stopped_status_when_reader_loop_exits

Validation

• cargo test --lib (new tests pass)
• cargo clippy --lib -- -D warnings
• cargo fmt --check
• npm run format:check
• npm run check (svelte-check)

Not fixed (needs separate PR)

• Follow-up messages silently dropped while agent is running (spawning_sessions guard blocks do_spawn for entire reader_loop duration)