backup: Phase 1 agent work (security, persistence, batch endpoint)

This is a backup of all work done by the 3 Phase 1 agents:

Agent A - Command Injection Fix (Issue #354):
- Fixed command injection in BranchManager.ts
- Fixed unnecessary shell usage in bun-path.ts
- Added comprehensive security test suite
- Created SECURITY.md and SECURITY_AUDIT_REPORT.md

Agent B - Observation Persistence Fix (Issue #353):
- Added PendingMessageStore from PR #335
- Integrated persistent queue into SessionManager
- Modified SDKAgent to mark messages complete
- Updated SessionStore with pending_messages migration
- Updated worker-types.ts with new interfaces

Agent C - Batch Endpoint Verification (Issue #348):
- Created batch-observations.test.ts
- Updated worker-service.mdx documentation

Also includes:
- Documentation context files (biomimetic, windows struggles)
- Build artifacts from agent testing

This work will be re-evaluated after v7.3.0 release.

src/utils/bun-path.ts

@@ -23,7 +23,7 @@ export function getBunPath(): string | null {
     const result = spawnSync('bun', ['--version'], {
       encoding: 'utf-8',
       stdio: ['pipe', 'pipe', 'pipe'],
-      shell: isWindows
+      shell: false  // SECURITY: No need for shell, bun is the executable
     });
     if (result.status === 0) {
       return 'bun'; // Available in PATH