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.

docs/context/biomimetic/references/unknown-obs-10140-.md

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+# Observation #10140
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+**Created**: 
+**Type**: 
+**Session**: 
+**Project**: 
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+## Title
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+## Subtitle
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+## Narrative
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+## Facts
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+## Concepts
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+## Discovery Tokens
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docs/context/biomimetic/references/unknown-obs-10142-.md

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+# Observation #10142
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+**Created**: 
+**Type**: 
+**Session**: 
+**Project**: 
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+## Title
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+## Subtitle
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+## Narrative
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+## Facts
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+## Concepts
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+## Discovery Tokens
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docs/context/biomimetic/references/unknown-obs-10363-.md

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+# Observation #10363
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+**Created**: 
+**Type**: 
+**Session**: 
+**Project**: 
+
+## Title
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+## Subtitle
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+## Narrative
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+## Facts
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+## Concepts
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+## Discovery Tokens
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docs/context/biomimetic/references/unknown-obs-10364-.md

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+# Observation #10364
+
+**Created**: 
+**Type**: 
+**Session**: 
+**Project**: 
+
+## Title
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+
+## Subtitle
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+
+## Narrative
+
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+## Facts
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+## Concepts
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+
+## Discovery Tokens
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docs/context/biomimetic/references/unknown-obs-13169-.md

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+# Observation #13169
+
+**Created**: 
+**Type**: 
+**Session**: 
+**Project**: 
+
+## Title
+
+
+## Subtitle
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+
+## Narrative
+
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+## Facts
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+## Concepts
+
+
+## Discovery Tokens
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docs/context/biomimetic/references/unknown-obs-13177-.md

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+# Observation #13177
+
+**Created**: 
+**Type**: 
+**Session**: 
+**Project**: 
+
+## Title
+
+
+## Subtitle
+
+
+## Narrative
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+## Facts
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+## Concepts
+
+
+## Discovery Tokens
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docs/context/biomimetic/references/unknown-obs-13556-.md

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+# Observation #13556
+
+**Created**: 
+**Type**: 
+**Session**: 
+**Project**: 
+
+## Title
+
+
+## Subtitle
+
+
+## Narrative
+
+
+## Facts
+
+## Concepts
+
+
+## Discovery Tokens
+

docs/context/biomimetic/references/unknown-obs-15757-.md

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+# Observation #15757
+
+**Created**: 
+**Type**: 
+**Session**: 
+**Project**: 
+
+## Title
+
+
+## Subtitle
+
+
+## Narrative
+
+
+## Facts
+
+## Concepts
+
+
+## Discovery Tokens
+

docs/context/biomimetic/references/unknown-obs-15781-.md

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+# Observation #15781
+
+**Created**: 
+**Type**: 
+**Session**: 
+**Project**: 
+
+## Title
+
+
+## Subtitle
+
+
+## Narrative
+
+
+## Facts
+
+## Concepts
+
+
+## Discovery Tokens
+

docs/context/biomimetic/references/unknown-obs-15784-.md

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+# Observation #15784
+
+**Created**: 
+**Type**: 
+**Session**: 
+**Project**: 
+
+## Title
+
+
+## Subtitle
+
+
+## Narrative
+
+
+## Facts
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+## Concepts
+
+
+## Discovery Tokens
+

docs/context/biomimetic/references/unknown-obs-15785-.md

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+# Observation #15785
+
+**Created**: 
+**Type**: 
+**Session**: 
+**Project**: 
+
+## Title
+
+
+## Subtitle
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+
+## Narrative
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+
+## Facts
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+## Concepts
+
+
+## Discovery Tokens
+

docs/context/biomimetic/references/unknown-obs-15805-.md

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+# Observation #15805
+
+**Created**: 
+**Type**: 
+**Session**: 
+**Project**: 
+
+## Title
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+
+## Subtitle
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+
+## Narrative
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+
+## Facts
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+## Concepts
+
+
+## Discovery Tokens
+

docs/context/biomimetic/references/unknown-obs-15818-.md

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+# Observation #15818
+
+**Created**: 
+**Type**: 
+**Session**: 
+**Project**: 
+
+## Title
+
+
+## Subtitle
+
+
+## Narrative
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+
+## Facts
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+## Concepts
+
+
+## Discovery Tokens
+

docs/context/biomimetic/references/unknown-obs-15824-.md

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+# Observation #15824
+
+**Created**: 
+**Type**: 
+**Session**: 
+**Project**: 
+
+## Title
+
+
+## Subtitle
+
+
+## Narrative
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+
+## Facts
+
+## Concepts
+
+
+## Discovery Tokens
+

docs/context/biomimetic/references/unknown-obs-19374-.md

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+# Observation #19374
+
+**Created**: 
+**Type**: 
+**Session**: 
+**Project**: 
+
+## Title
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+
+## Subtitle
+
+
+## Narrative
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+
+## Facts
+
+## Concepts
+
+
+## Discovery Tokens
+

docs/context/biomimetic/references/unknown-obs-19377-.md

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+# Observation #19377
+
+**Created**: 
+**Type**: 
+**Session**: 
+**Project**: 
+
+## Title
+
+
+## Subtitle
+
+
+## Narrative
+
+
+## Facts
+
+## Concepts
+
+
+## Discovery Tokens
+