feat: add project repository version control module

[grantf04]

@algora-pbc /claim #10

Closes #10

What this adds

Adds a self-contained project-repository-version-control/ module for scientific project repositories: structured components, hash manifests, commits, branches, forks, merge requests, reproducibility checks, citations, export metadata, JSON APIs, tests, and a reviewer dashboard.

Requirement mapping

• Repository structure and components → implemented in demoRepository.files with manuscript, data, code, notebooks, results, protocols, and metadata.
• File and metadata versioning → implemented by hash manifests, commit history, branch timelines, and DOI-version metadata in src/repository-core.js.
• Collaboration and forking → implemented through fork attribution, merge request summaries, reviewers, discussion, and branch diffs.
• In-browser editors and diffs → represented through Markdown/notebook-aware diff summaries and dashboard review surfaces.
• Computation-aware reproducibility → implemented by runReproducibilityCheck for pipeline, raw data hash, expected outputs, metadata schema, and sandbox status.
• Repository identifiers and citation → implemented by DOI generation plus APA, MLA, and BibTeX citations.
• Programmatic access and export → implemented by API routes in src/server.js and buildExportBundle.

How to verify in under 5 minutes

cd project-repository-version-control
npm test
npm start

Open http://localhost:4129 and verify the dashboard shows repository DOI, component manifest, merge request diff summaries, reproducibility checks, citation text, and export metadata.

Optional API smoke checks:

curl -s http://localhost:4129/api/dashboard
curl -s http://localhost:4129/api/repositories/repo-organoid-response/manifest
curl -s "http://localhost:4129/api/repositories/repo-organoid-response/citation?style=BibTeX"

Validation

Commands run:

• npm test - 4 tests passing
• curl -s http://localhost:4129/api/dashboard - returns repository title, passed reproducibility status, and export bundle filename
• curl -s "http://localhost:4129/api/repositories/repo-organoid-response/citation?style=BibTeX" - returns BibTeX dataset citation
• curl -i -s http://localhost:4129/package.json - returns 404 without crashing the server
• Browser demo verified at http://127.0.0.1:4129/: repository, version-control, reproducibility, and citation/export panels render with 0 console errors
• ffprobe verified the committed demo video is 1280x760 and 8 seconds long

Demo

• Short demo video: project-repository-version-control-demo.mp4
• Screenshot: dashboard.png
• Demo script: project-repository-version-control/docs/demo-script.md

Scope

This PR is intentionally self-contained under project-repository-version-control/ and avoids unrelated root-level changes except adding the module link to the root README.