[codex] Add discussion sidebar audit

collaborative-discussion-sidebar-audit/README.md

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+# Collaborative Discussion Sidebar Audit
+
+This package adds a focused readiness layer for the real-time collaborative research editor requested in SCIBASE issue #12. It does not implement a broad editor shell, notebook runtime, reference formatter, lock recovery system, or figure/table workflow. Instead, it covers the issue requirement for a document chat or discussion sidebar per file or section.
+
+The audit model checks whether sidebar discussions are safe to export during an active manuscript review:
+
+- section and file scoped discussion threads
+- open blockers, stale conversations, and unresolved reviewer tasks
+- pinned sources and citation evidence for decisions
+- conflicting accepted decisions on the same section/topic
+- locked-section owner and reviewer participation
+- deterministic handoff packets for review, export, and version history
+
+## Run
+
+```sh
+npm test
+npm run demo
+npm run demo:video
+```
+
+`npm run demo` writes a JSON audit report and an SVG storyboard to `docs/`. `npm run demo:video` renders a short MP4 demo for reviewers.
+
+## Why This Slice Matters
+
+In a collaborative scientific editor, the sidebar is not just chat. It becomes the record of why a section changed, which source supports the decision, who still needs to respond, and what must be preserved when the document is exported or reviewed later. This package gives that workflow deterministic checks and a compact export packet before the larger editor UI is wired in.

collaborative-discussion-sidebar-audit/docs/discussion-sidebar-audit-report.json

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+{
+  "ready": false,
+  "project": {
+    "id": "scibase-paper-alpha",
+    "title": "Multimodal biomarker screening draft",
+    "reviewRound": "methods-freeze"
+  },
+  "counts": {
+    "sections": 3,
+    "threads": 4,
+    "decisions": 3,
+    "blockers": 5,
+    "warnings": 3,
+    "reviewerTasks": 1
+  },
+  "sidebarCoverage": {
+    "scopedSections": 3,
+    "totalSections": 3,
+    "resolvedThreads": 2,
+    "totalThreads": 4,
+    "pinnedSources": 3,
+    "unscopedThreads": 1
+  },
+  "findings": [
+    {
+      "severity": "blocker",
+      "code": "open-blocker",
+      "message": "Thread thr-methods-blocker is marked blocking and is still open.",
+      "context": {
+        "threadId": "thr-methods-blocker"
+      }
+    },
+    {
+      "severity": "blocker",
+      "code": "stale-thread",
+      "message": "Thread thr-methods-blocker has been idle for 8 days.",
+      "context": {
+        "threadId": "thr-methods-blocker",
+        "staleDays": 8
+      }
+    },
+    {
+      "severity": "warning",
+      "code": "locked-section-missing-review-role",
+      "message": "Thread thr-methods-blocker on locked section sec-methods is missing reviewer participation.",
+      "context": {
+        "threadId": "thr-methods-blocker",
+        "sectionId": "sec-methods",
+        "missingRoles": [
+          "reviewer"
+        ]
+      }
+    },
+    {
+      "severity": "warning",
+      "code": "locked-section-missing-review-role",
+      "message": "Thread thr-results-decision on locked section sec-results is missing owner participation.",
+      "context": {
+        "threadId": "thr-results-decision",
+        "sectionId": "sec-results",
+        "missingRoles": [
+          "owner"
+        ]
+      }
+    },
+    {
+      "severity": "blocker",
+      "code": "unsafe-pinned-source",
+      "message": "Thread thr-file-evidence pins retracted source src-old-preprint.",
+      "context": {
+        "threadId": "thr-file-evidence",
+        "sourceId": "src-old-preprint",
+        "sourceStatus": "retracted"
+      }
+    },
+    {
+      "severity": "blocker",
+      "code": "unknown-scope",
+      "message": "Thread thr-orphan-sidebar is attached to an unknown section scope.",
+      "context": {
+        "threadId": "thr-orphan-sidebar",
+        "scopeId": "sec-supplement"
+      }
+    },
+    {
+      "severity": "warning",
+      "code": "decision-missing-source",
+      "message": "Decision dec-methods-draft has no pinned source evidence.",
+      "context": {
+        "decisionId": "dec-methods-draft"
+      }
+    },
+    {
+      "severity": "blocker",
+      "code": "conflicting-decisions",
+      "message": "Multiple active decisions compete for sec-results:model-summary.",
+      "context": {
+        "decisionIds": [
+          "dec-results-adjusted",
+          "dec-results-conflict"
+        ]
+      }
+    }
+  ],
+  "reviewerTasks": [
+    {
+      "id": "thr-methods-blocker:resolve-blocker",
+      "threadId": "thr-methods-blocker",
+      "ownerId": "u-ada",
+      "title": "Resolve blocker: Resolve assay exclusion criteria",
+      "priority": "high"
+    }
+  ],
+  "exportPacket": {
+    "generatedAt": "2026-05-16T17:00:00.000Z",
+    "packetHash": "ebc3395f938f09def2f2aaa386b8e119a7c73314f3d7331e04e486b7a5fb638f",
+    "auditDigest": "scibase-paper-alpha:5:3:1:ebc3395f938f",
+    "entries": [
+      {
+        "threadId": "thr-file-evidence",
+        "title": "Remove unsupported background citation",
+        "scopeType": "file",
+        "scopeId": "paper/introduction.md",
+        "sectionTitle": "Introduction",
+        "status": "resolved",
+        "blocking": false,
+        "ownerId": "u-max",
+        "participantIds": [
+          "u-ada",
+          "u-max"
+        ],
+        "pinnedSourceIds": [
+          "src-old-preprint"
+        ],
+        "decisionIds": []
+      },
+      {
+        "threadId": "thr-methods-blocker",
+        "title": "Resolve assay exclusion criteria",
+        "scopeType": "section",
+        "scopeId": "sec-methods",
+        "sectionTitle": "Methods",
+        "status": "open",
+        "blocking": true,
+        "ownerId": "u-ada",
+        "participantIds": [
+          "u-ada"
+        ],
+        "pinnedSourceIds": [
+          "src-protocol"
+        ],
+        "decisionIds": [
+          "dec-methods-draft"
+        ]
+      },
+      {
+        "threadId": "thr-orphan-sidebar",
+        "title": "Unattached sidebar note",
+        "scopeType": "section",
+        "scopeId": "sec-supplement",
+        "sectionTitle": null,
+        "status": "open",
+        "blocking": false,
+        "ownerId": "u-max",
+        "participantIds": [
+          "u-max"
+        ],
+        "pinnedSourceIds": [
+          "src-dataset"
+        ],
+        "decisionIds": []
+      },
+      {
+        "threadId": "thr-results-decision",
+        "title": "Accept adjusted model summary",
+        "scopeType": "section",
+        "scopeId": "sec-results",
+        "sectionTitle": "Results",
+        "status": "resolved",
+        "blocking": false,
+        "ownerId": "u-rin",
+        "participantIds": [
+          "u-max",
+          "u-rin"
+        ],
+        "pinnedSourceIds": [
+          "src-dataset"
+        ],
+        "decisionIds": [
+          "dec-results-adjusted",
+          "dec-results-conflict"
+        ]
+      }
+    ]
+  }
+}

collaborative-discussion-sidebar-audit/docs/requirement-map.md

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+# Requirement Map
+
+This package targets the "Document chat or discussion sidebar per file or section" requirement from SCIBASE issue #12.
+
+| Issue capability | Coverage in this package |
+| --- | --- |
+| Real-time collaboration readiness | Validates sidebar participants, open blockers, reviewer ownership, and locked-section participation before export. |
+| Section and file comments | Models threads scoped to either manuscript sections or file paths, then flags orphaned threads. |
+| Suggestions, decisions, and discussion history | Records accepted/proposed decisions and detects conflicting active decisions for the same section/topic. |
+| Version history and autosave handoff | Emits a deterministic export packet with stable hash and audit digest suitable for snapshot history. |
+| Scientific source traceability | Requires pinned source evidence for decisions and blocks unsafe or missing sources. |
+| Reviewer task management | Converts unresolved blocking threads into explicit reviewer tasks with owners and priority. |
+
+The slice is deliberately narrow so it can be reviewed independently of larger editor, notebook, reference-formatting, and figure/table implementations.

collaborative-discussion-sidebar-audit/package.json

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+{
+  "name": "collaborative-discussion-sidebar-audit",
+  "version": "1.0.0",
+  "description": "Section-scoped discussion sidebar audit tools for a collaborative research editor.",
+  "type": "module",
+  "private": true,
+  "scripts": {
+    "test": "node test/collaborative-discussion-sidebar-audit.test.js",
+    "demo": "node scripts/demo.js",
+    "demo:video": "mkdir -p docs && clang -fobjc-arc -framework Foundation -framework AppKit -framework AVFoundation -framework CoreMedia -framework CoreVideo scripts/render-demo-video.m -o /tmp/discussion-sidebar-demo && /tmp/discussion-sidebar-demo docs/demo.mp4"
+  },
+  "exports": {
+    ".": "./src/collaborative-discussion-sidebar-audit.js"
+  }
+}