fix(check-update): detect corpus drift beyond the manifest

[TPAteeq]

Summary

• Make graphify check-update scan the current corpus using Graphify's normal discovery and ignore rules.
• Report added, changed, and removed file counts.
• Use AST hashes for code and semantic hashes for documents, papers, images, and videos.
• Continue honoring the existing needs_update flag.
• Print an explicit up-to-date status when no drift exists.
• Preserve cron-safe exit behavior.

Validation

• 3120 passed, 30 skipped
• ruff check passed
• Added coverage for added, changed, removed, ignored, AST-only, and semantic-staleness cases
• graphify update . completed successfully

Closes #1765