feat: add project repository version control module

README.md

@@ -1,2 +1,6 @@
 # deepevents.ai
 deepevents.ai main codebase
+
+## Modules
+
+- [`project-repository-version-control`](./project-repository-version-control) - runnable prototype for citable scientific project repositories, version control, reproducibility checks, and export metadata.

project-repository-version-control/README.md

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+# Project Repository & Version Control
+
+This module is a self-contained implementation for SCIBASE.AI issue #10. It models the scientific project repository as a citable, versioned, reproducible workspace with manuscript, data, code, notebook, result, protocol, and metadata components.
+
+## What It Covers
+
+- Repository structure for `manuscript/`, `data/`, `code/`, `notebooks/`, `results/`, `protocols/`, and `metadata.json`.
+- Hash-based manifest generation for file integrity and reproducible export bundles.
+- Commit history, branch timelines, semantic version DOI metadata, forks, attribution, and merge request summaries.
+- Markdown/notebook-aware diff summaries for review workflows.
+- Computation-aware reproducibility checks for pipeline presence, raw data hashes, expected outputs, metadata schema, and sandbox execution.
+- Auto-generated APA, MLA, and BibTeX citations.
+- JSON API and browser dashboard for reviewer smoke testing.
+
+## Run Locally
+
+```bash
+cd project-repository-version-control
+npm test
+npm start
+```
+
+Then open `http://localhost:4129`.
+
+## API Surface
+
+- `GET /api/dashboard`
+- `GET /api/repositories/repo-organoid-response`
+- `GET /api/repositories/repo-organoid-response/manifest`
+- `GET /api/repositories/repo-organoid-response/merge-request`
+- `GET /api/repositories/repo-organoid-response/reproducibility`
+- `GET /api/repositories/repo-organoid-response/citation?style=APA|MLA|BibTeX`
+- `GET /api/repositories/repo-organoid-response/export`
+
+## Requirement Mapping
+
+- Repository components: represented in `demoRepository.files`.
+- File and metadata versioning: implemented by `buildManifest`, hash generation, branches, and commits.
+- Collaboration and forking: represented by `forks`, `mergeRequests`, branch timelines, discussion, and reviewer metadata.
+- In-browser editors and diffs: implemented as Markdown/notebook-aware diff summaries and dashboard review surfaces.
+- Computation-aware reproducibility: implemented by `runReproducibilityCheck`.
+- Repository identifiers and citation: implemented by DOI generation and `buildCitation`.
+- Programmatic access and export: implemented by the JSON API and `buildExportBundle`.
+
+## Verification
+
+```bash
+npm test
+node src/server.js
+```
+
+Optional smoke checks:
+
+```bash
+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"
+```
+
+Demo artifacts are committed under `docs/demo/`, including `dashboard.png` and `project-repository-version-control-demo.mp4`.

project-repository-version-control/docs/demo-script.md

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+# Demo Script
+
+1. Run `npm test` to verify manifest, commit, diff, reproducibility, citation, and export logic.
+2. Run `npm start` and open `http://localhost:4129`.
+3. Confirm the dashboard shows repository DOI, file count, component list, and integrity hash.
+4. Inspect the merge request card for changed files and Markdown/notebook-aware diff types.
+5. Confirm the reproducibility checks all pass.
+6. Review the generated citation and export bundle metadata.

project-repository-version-control/package.json

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+{
+  "name": "@scibase/project-repository-version-control",
+  "version": "0.1.0",
+  "private": true,
+  "description": "Self-contained scientific project repository and version-control prototype for SCIBASE.AI issue #10.",
+  "type": "module",
+  "scripts": {
+    "start": "node src/server.js",
+    "test": "node --test test/*.test.js"
+  },
+  "engines": {
+    "node": ">=20"
+  }
+}

project-repository-version-control/public/app.js

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+const dashboard = await fetch("/api/dashboard").then((response) => response.json());
+
+document.querySelector("#repoTitle").textContent = dashboard.manifest.title;
+document.querySelector("#manifest").innerHTML = [
+  stat("DOI", dashboard.manifest.doi),
+  stat("Files", dashboard.manifest.files.length),
+  stat("Components", Object.keys(dashboard.manifest.components).join(", ")),
+  stat("Integrity", dashboard.manifest.integrityHash.slice(0, 16))
+].join("");
+
+document.querySelector("#mergeRequest").innerHTML = `
+  <div class="callout">
+    <strong>${dashboard.mergeRequest.id}</strong>
+    <span>${dashboard.mergeRequest.status}</span>
+  </div>
+  <ul>
+    ${dashboard.mergeRequest.diffs.map((diff) => `<li>${diff.path} · ${diff.type} · ${diff.hunks.length} hunks</li>`).join("")}
+  </ul>
+`;
+
+document.querySelector("#checks").innerHTML = `
+  <div class="status ${dashboard.reproducibility.status}">${dashboard.reproducibility.status}</div>
+  <ul>
+    ${dashboard.reproducibility.checks.map((check) => `<li>${check.passed ? "PASS" : "FAIL"} · ${check.name}</li>`).join("")}
+  </ul>
+`;
+
+document.querySelector("#citation").textContent = dashboard.citation.apa;
+document.querySelector("#export").textContent = `${dashboard.exportBundle.fileName} · ${dashboard.exportBundle.cliCommand}`;
+
+function stat(label, value) {
+  return `<div><span>${label}</span><strong>${String(value)}</strong></div>`;
+}

project-repository-version-control/public/index.html

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+<!doctype html>
+<html lang="en">
+  <head>
+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1" />
+    <title>SCIBASE Project Repository</title>
+    <link rel="stylesheet" href="/styles.css" />
+  </head>
+  <body>
+    <main class="shell">
+      <header>
+        <p>SCIBASE.AI / issue #10</p>
+        <h1>Project Repository & Version Control</h1>
+      </header>
+      <section class="grid">
+        <article class="panel hero">
+          <p class="label">Repository</p>
+          <h2 id="repoTitle">Loading...</h2>
+          <div id="manifest" class="stats"></div>
+        </article>
+        <article class="panel">
+          <p class="label">Version Control</p>
+          <h2>Commit history and merge requests</h2>
+          <div id="mergeRequest"></div>
+        </article>
+        <article class="panel">
+          <p class="label">Reproducibility</p>
+          <h2>Sandbox validation</h2>
+          <div id="checks"></div>
+        </article>
+        <article class="panel">
+          <p class="label">Citation & Export</p>
+          <h2>Citable version bundle</h2>
+          <code id="citation"></code>
+          <p id="export"></p>
+        </article>
+      </section>
+    </main>
+    <script type="module" src="/app.js"></script>
+  </body>
+</html>

project-repository-version-control/public/styles.css

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+:root {
+  --ink: #111615;
+  --muted: #64706d;
+  --line: #d7ded9;
+  --paper: #f3f6f1;
+  --panel: #ffffff;
+  --green: #17664c;
+  --blue: #285f8f;
+}
+
+* {
+  box-sizing: border-box;
+}
+
+body {
+  margin: 0;
+  background: var(--paper);
+  color: var(--ink);
+  font-family: Inter, ui-sans-serif, system-ui, -apple-system, BlinkMacSystemFont, "Segoe UI", sans-serif;
+}
+
+.shell {
+  max-width: 1280px;
+  margin: 0 auto;
+  padding: 32px;
+}
+
+header {
+  display: flex;
+  align-items: end;
+  justify-content: space-between;
+  gap: 24px;
+  margin-bottom: 24px;
+}
+
+header p,
+.label {
+  color: var(--muted);
+  font-size: 12px;
+  font-weight: 900;
+  letter-spacing: 0.08em;
+  text-transform: uppercase;
+}
+
+h1,
+h2,
+p {
+  margin: 0;
+}
+
+h1 {
+  max-width: 820px;
+  font-size: clamp(38px, 6vw, 76px);
+  line-height: 0.95;
+  letter-spacing: 0;
+}
+
+h2 {
+  margin-top: 8px;
+  font-size: 24px;
+}
+
+.grid {
+  display: grid;
+  grid-template-columns: 1.1fr 0.9fr;
+  gap: 16px;
+}
+
+.panel {
+  min-height: 260px;
+  border: 1px solid var(--line);
+  background: var(--panel);
+  padding: 24px;
+}
+
+.hero {
+  grid-row: span 2;
+}
+
+.stats {
+  display: grid;
+  gap: 12px;
+  margin-top: 26px;
+}
+
+.stats div,
+.callout,
+li,
+code,
+#export,
+.status {
+  border-top: 1px solid var(--line);
+  padding-top: 12px;
+}
+
+.stats span {
+  display: block;
+  color: var(--muted);
+  font-size: 12px;
+  font-weight: 900;
+  text-transform: uppercase;
+}
+
+.stats strong {
+  display: block;
+  margin-top: 5px;
+  overflow-wrap: anywhere;
+}
+
+.callout {
+  display: flex;
+  justify-content: space-between;
+  gap: 14px;
+  margin-top: 18px;
+}
+
+.callout span,
+.status {
+  color: var(--green);
+  font-weight: 900;
+  text-transform: uppercase;
+}
+
+ul {
+  margin: 18px 0 0;
+  padding: 0;
+  list-style: none;
+}
+
+li {
+  line-height: 1.35;
+}
+
+code,
+#export {
+  display: block;
+  margin-top: 18px;
+  color: var(--blue);
+  line-height: 1.5;
+  white-space: normal;
+}
+
+@media (max-width: 820px) {
+  .shell {
+    padding: 18px;
+  }
+
+  header,
+  .grid {
+    display: grid;
+    grid-template-columns: 1fr;
+  }
+}