refactor: extract agent bounded context + fix SSE comments + cleanup unused

- Extract src/lib/agent/ bounded context with types, registry, messaging
- Add comments_count to BeadIssue for SSE comment detection
- Create batch endpoints for mail/reservations APIs
- Add memory validation to session-preflight
- Remove unused empty dirs (mockup, sessions, timeline)
- Move stashes to docs/references, gitignore them

skills/beadboard-driver/tests/run-tests.mjs

@@ -17,6 +17,7 @@ const tests = [
   path.join(__dirname, 'diagnose-env.contract.test.mjs'),
   path.join(__dirname, 'heal-common-issues.contract.test.mjs'),
   path.join(__dirname, 'ensure-project-context.contract.test.mjs'),
+  path.join(__dirname, 'setup-mail-delegate.contract.test.mjs'),
 ];
 
 const child = spawn(process.execPath, ['--test', ...tests], {