Add collaborative editor governance module

collaborative-editor-governance/README.md

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+# Collaborative Editor Governance
+
+Self-contained collaborative research editor governance milestone for [SCIBASE.AI issue #12](https://github.com/SCIBASE-AI/SCIBASE.AI/issues/12).
+
+The issue asks for a real-time collaborative research editor. This module focuses on a reviewable core for deterministic operation replay and editorial governance: typed scientific blocks, locks, comments, suggestions, tasks, snapshots, collaborator presence, and publication outline export.
+
+## What It Adds
+
+- Scientific document blocks with Markdown, LaTeX, code metadata, references, and section headings.
+- Deterministic operation handling for block inserts, updates, deletes, comments, suggestions, and tasks.
+- Section-lock enforcement that rejects edits from non-owners.
+- Inline comment and suggestion state for peer review.
+- Autosave/version snapshot with content hash and open review counts.
+- Open-task dashboard and collaborator presence summary.
+- Scientific formatting summary covering LaTeX, code highlighting, notebook blocks, reference-provider metadata, citation resolution, and publication templates.
+- Offline collaboration conflict report for queued client operations, stale block versions, section-lock conflicts, missing review targets, safe suggestion conversion, restore snapshots, and audit hashes.
+- Publication outline export with section block types, word counts, and export hash.
+- Sample document fixture, tests, requirement map, CLI demo, and short demo GIF.
+
+## Run
+
+```bash
+cd collaborative-editor-governance
+npm run check
+npm test
+npm run demo
+```
+
+Expected demo shape:
+
+```json
+{
+  "title": "Longitudinal microbiome shifts after coastal flooding",
+  "acceptedOperations": 3,
+  "rejectedOperations": 1,
+  "readyForSubmission": false,
+  "formatting": {
+    "supportsLatex": true,
+    "referenceManager": {
+      "providers": ["zotero"],
+      "unresolvedCitations": []
+    }
+  },
+  "offlineConflicts": {
+    "queueCount": 1,
+    "conflictCodes": ["REVIEW_TARGET_MISSING", "SECTION_LOCK_CONFLICT", "STALE_BLOCK_VERSION"]
+  },
+  "outlineHash": "..."
+}
+```
+
+## Demo Artifact
+
+See [docs/demo.gif](docs/demo.gif) for a short visual walkthrough. The SVG source is included at [docs/demo.svg](docs/demo.svg).
+
+## Files
+
+- `src/editor-governance.js` - operation replay, locks, snapshots, dashboard, offline conflict resolution, and outline export.
+- `data/sample-document.json` - reviewable scientific document fixture.
+- `test/editor-governance.test.js` - dependency-free Node tests.
+- `scripts/demo.js` - CLI demo.
+- `docs/issue-12-requirement-map.md` - maps the implementation to bounty requirements.
+
+## AI-Assisted Disclosure
+
+This contribution was produced with AI assistance and manually verified with the local commands above.

collaborative-editor-governance/data/sample-document.json

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+{
+  "document": {
+    "id": "doc-flooding-microbiome",
+    "title": "Longitudinal microbiome shifts after coastal flooding",
+    "collaborators": [
+      { "id": "u-1", "name": "Principal investigator", "role": "owner" },
+      { "id": "u-2", "name": "Methods reviewer", "role": "reviewer" },
+      { "id": "u-3", "name": "Data analyst", "role": "editor" }
+    ],
+    "blocks": [
+      {
+        "id": "block-abstract",
+        "sectionId": "abstract",
+        "type": "markdown",
+        "content": "We report longitudinal microbiome shifts after coastal flooding.",
+        "metadata": { "heading": "Abstract" }
+      },
+      {
+        "id": "block-methods",
+        "sectionId": "methods",
+        "type": "markdown",
+        "content": "Samples were collected monthly and sequenced with a documented protocol @smith2026.",
+        "metadata": { "heading": "Methods" }
+      },
+      {
+        "id": "block-equation",
+        "sectionId": "methods",
+        "type": "latex",
+        "content": "$H = -\\sum_i p_i \\log(p_i)$",
+        "metadata": { "label": "eq:diversity" }
+      },
+      {
+        "id": "block-code",
+        "sectionId": "methods",
+        "type": "code",
+        "content": "normalize_counts(samples)",
+        "metadata": { "language": "python" }
+      }
+    ],
+    "comments": [],
+    "suggestions": [],
+    "locks": [
+      { "sectionId": "methods", "ownerId": "u-2", "status": "active" }
+    ],
+    "tasks": [
+      { "id": "task-1", "title": "Attach data dictionary", "assigneeId": "u-3", "status": "open" }
+    ],
+    "presence": [
+      {
+        "userId": "u-1",
+        "name": "Principal investigator",
+        "sectionId": "abstract",
+        "cursorBlockId": "block-abstract",
+        "lastSeenAt": "2026-05-14T07:00:00Z"
+      },
+      {
+        "userId": "u-2",
+        "name": "Methods reviewer",
+        "sectionId": "methods",
+        "cursorBlockId": "block-methods",
+        "lastSeenAt": "2026-05-14T07:00:00Z"
+      }
+    ],
+    "references": [
+      {
+        "key": "smith2026",
+        "provider": "zotero",
+        "title": "Flooding exposure sequencing protocol",
+        "doi": "10.5555/example"
+      }
+    ],
+    "publicationTemplates": [
+      {
+        "id": "nature-methods",
+        "name": "Nature Methods",
+        "style": "nature",
+        "requiredSections": ["abstract", "methods", "results", "references"]
+      }
+    ],
+    "versions": [],
+    "offlineQueues": [
+      {
+        "clientId": "offline-u-3",
+        "baseVersionId": "snapshot-draft-1",
+        "baseContentHash": "draft-base-hash",
+        "operations": [
+          {
+            "type": "update-block",
+            "actorId": "u-3",
+            "blockId": "block-abstract",
+            "baseBlockHash": "stale-abstract-hash",
+            "content": "We report flood-linked microbiome shifts with a larger validation cohort.",
+            "rebasedSuggestionId": "suggestion-offline-abstract"
+          },
+          {
+            "type": "update-block",
+            "actorId": "u-3",
+            "blockId": "block-methods",
+            "baseBlockHash": "stale-methods-hash",
+            "content": "Offline edit should wait because the methods section is locked."
+          },
+          {
+            "type": "comment",
+            "id": "comment-missing-block",
+            "actorId": "u-3",
+            "blockId": "block-removed",
+            "body": "This comment targets a block that disappeared while offline."
+          },
+          {
+            "type": "insert-block",
+            "actorId": "u-3",
+            "index": 4,
+            "block": {
+              "id": "block-offline-note",
+              "sectionId": "discussion",
+              "type": "markdown",
+              "content": "Offline reviewer note preserved after reconnect.",
+              "metadata": { "heading": "Discussion" }
+            }
+          }
+        ]
+      }
+    ]
+  },
+  "operations": [
+    {
+      "type": "comment",
+      "id": "comment-1",
+      "actorId": "u-2",
+      "blockId": "block-methods",
+      "body": "Please cite the sequencing protocol and include reagent version."
+    },
+    {
+      "type": "suggestion",
+      "id": "suggestion-1",
+      "actorId": "u-2",
+      "blockId": "block-methods",
+      "proposedContent": "Samples were collected monthly and sequenced with protocol v2.1."
+    },
+    {
+      "type": "update-block",
+      "actorId": "u-3",
+      "blockId": "block-methods",
+      "content": "This edit should be rejected while the methods section is locked."
+    },
+    {
+      "type": "insert-block",
+      "actorId": "u-1",
+      "index": 3,
+      "block": {
+        "id": "block-results",
+        "sectionId": "results",
+        "type": "markdown",
+        "content": "Observed diversity increased after flooding and moved toward baseline after remediation.",
+        "metadata": { "heading": "Results" }
+      }
+    }
+  ]
+}

collaborative-editor-governance/docs/issue-12-requirement-map.md

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+# Issue #12 Requirement Map
+
+This module is a deterministic milestone for SCIBASE issue #12, Real-time collaborative research editor & interface. It focuses on review governance, operation replay, and offline conflict handling for scientific documents.
+
+| Issue requirement | Implementation |
+| --- | --- |
+| Scientific document blocks | Blocks include `markdown`, `latex`, `code`, section IDs, headings, language metadata, and publication outline export. |
+| Markdown and LaTeX formatting | `buildScientificFormattingSummary()` reports Markdown blocks and LaTeX/equation support from typed blocks and inline equation syntax. |
+| Reference manager integration | Document references preserve provider metadata such as Zotero/BibTeX source, cited keys, and unresolved citations. |
+| Publication templates | Publication template metadata captures style names and required sections for common journal formats. |
+| Code snippet highlighting | Code blocks carry language metadata and are reported in the scientific formatting summary. |
+| Real-time operation application | `applyOperation()` and `applyOperationBatch()` deterministically apply insert, update, delete, comment, suggestion, and task operations. |
+| Comments and suggestions | Comment and suggestion operations are stored with block links, actor IDs, and open/pending status. |
+| Section locks | `isSectionLocked()` rejects edits from non-owners while allowing the lock owner to edit. |
+| Offline/local caching conflict recovery | `rebaseOfflineQueue()` and `buildOfflineConflictReport()` process queued offline edits, detect stale block versions, preserve safe edits as suggestions, flag missing review targets, and create restore-ready snapshots. |
+| Version history and autosave | `createVersionSnapshot()` records block count, open review items, content hash, and timestamp. |
+| Task workflow | Task operations and dashboard open-task reporting support editorial handoff. |
+| Collaborator presence | `buildPresenceSummary()` turns presence data into reviewer-ready cursor and staleness state. |
+| Publication outline export | `exportPublicationOutline()` summarizes sections, block types, word counts, and export hash. |
+| Reviewer demo | `npm run demo` prints accepted/rejected operation counts, snapshot, offline conflict codes, dashboard sections, and outline hash. |
+
+## Verification
+
+```bash
+npm run check
+npm test
+npm run demo
+```
+
+The module is dependency-free and isolated under `collaborative-editor-governance/`.

collaborative-editor-governance/package.json

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+{
+  "name": "scibase-collaborative-editor-governance",
+  "version": "0.1.0",
+  "private": true,
+  "description": "Deterministic collaborative research editor governance milestone for SCIBASE issue #12.",
+  "type": "commonjs",
+  "scripts": {
+    "check": "node --check src/editor-governance.js && node --check scripts/demo.js && node --check test/editor-governance.test.js",
+    "demo": "node scripts/demo.js",
+    "test": "node test/editor-governance.test.js"
+  }
+}

collaborative-editor-governance/scripts/demo.js

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+"use strict";
+
+const sample = require("../data/sample-document.json");
+const { buildCollaborativeEditorPacket } = require("../src/editor-governance");
+
+const packet = buildCollaborativeEditorPacket(sample.document, sample.operations);
+
+console.log(
+  JSON.stringify(
+    {
+      title: packet.document.title,
+      acceptedOperations: packet.operationResults.filter((result) => result.accepted).length,
+      rejectedOperations: packet.operationResults.filter((result) => !result.accepted).length,
+      snapshot: packet.snapshot,
+      readyForSubmission: packet.dashboard.readyForSubmission,
+      formatting: packet.formatting,
+      offlineConflicts: {
+        queueCount: packet.offlineConflicts.queueCount,
+        appliedCount: packet.offlineConflicts.appliedCount,
+        conflictCount: packet.offlineConflicts.conflictCount,
+        conflictCodes: packet.offlineConflicts.conflictCodes,
+      },
+      sections: packet.dashboard.sections,
+      outlineHash: packet.outline.exportHash,
+    },
+    null,
+    2,
+  ),
+);