Remove unused files and clean up configs

[nicholaspsmith]

Summary

This PR removes stale and unused files that are no longer needed for the project:

• Deleted ARCHITECTURE.md - outdated architecture documentation
• Deleted MIGRATION_GUIDE.md - no longer used migration guide
• Deleted tests/helpers/mock-embeddings.ts - unused test helper
• Cleaned up knip.config.ts by removing 14 lines of stale ignore rules
• Fixed broken ARCHITECTURE.md reference in README.md

Why

These files are no longer maintained or referenced in the codebase. Removing them:

• Reduces repository clutter and maintenance burden
• Eliminates broken documentation references
• Removes unused test utilities
• Cleans up stale configuration entries

Test plan

• All cleanup changes are file deletions and config simplifications
• No functional code changes, no new tests needed
• Verify CI passes after merge