COD-54: support ZIP bundle versioning

[code2rich]

Summary

• preserve file ID, share key, visibility, and complete directory history when a same-name bundle ZIP is uploaded
• overwrite batch ZIP entries individually and reject ambiguous duplicate basenames or storage-shape mismatches
• support bundle history render/assets/content/download/restore/delete/pruning across Web, multipart, MCP, and base64 paths
• add bundle-aware version metadata migration, storage lifecycle helpers, UI support, documentation, and regression coverage

Root cause

ZIP bundles are directory-backed, but the previous version model and overwrite endpoints treated every version as a single file. Automatic ZIP uploads created duplicates, while explicit overwrite could leave bundle metadata pointing at a raw ZIP and break rendering.

Validation

• node --test test/integration/zip-versions.test.js — 6 passed
• focused ZIP/version/security/usage/CLI tests — 89 passed
• npm test — 352 passed
• npm run lint
• npm run build
• git diff --check

Closes COD-54