Cleanup prompts and add workflows

.github/workflows/gh-aw-autonomy-atomicity-analyzer.md

@@ -0,0 +1,159 @@
+---
+inlined-imports: true
+name: "Autonomy Atomicity Analyzer"
+description: "Find patterns that block concurrent development by multiple agents or developers"
+imports:
+  - gh-aw-fragments/elastic-tools.md
+  - gh-aw-fragments/runtime-setup.md
+  - gh-aw-fragments/formatting.md
+  - gh-aw-fragments/rigor.md
+  - gh-aw-fragments/mcp-pagination.md
+  - gh-aw-fragments/messages-footer.md
+  - gh-aw-fragments/safe-output-create-issue.md
+  - gh-aw-fragments/previous-findings.md
+  - gh-aw-fragments/best-of-three-investigation.md
+  - gh-aw-fragments/scheduled-audit.md
+  - gh-aw-fragments/network-ecosystems.md
+engine:
+  id: copilot
+  model: ${{ inputs.model }}
+on:
+  workflow_call:
+    inputs:
+      model:
+        description: "AI model to use"
+        type: string
+        required: false
+        default: "gpt-5.3-codex"
+      additional-instructions:
+        description: "Repo-specific instructions appended to the agent prompt"
+        type: string
+        required: false
+        default: ""
+      setup-commands:
+        description: "Shell commands to run before the agent starts (dependency install, build, etc.)"
+        type: string
+        required: false
+        default: ""
+      allowed-bot-users:
+        description: "Allowlisted bot actor usernames (comma-separated)"
+        type: string
+        required: false
+        default: "github-actions[bot]"
+      messages-footer:
+        description: "Footer appended to all agent comments and reviews"
+        type: string
+        required: false
+        default: ""
+      title-prefix:
+        description: "Title prefix for created issues (e.g. '[autonomy-atomicity]')"
+        type: string
+        required: false
+        default: "[autonomy-atomicity]"
+    secrets:
+      COPILOT_GITHUB_TOKEN:
+        required: true
+  roles: [admin, maintainer, write]
+  bots:
+    - "${{ inputs.allowed-bot-users }}"
+concurrency:
+  group: autonomy-atomicity-analyzer
+  cancel-in-progress: true
+permissions:
+  contents: read
+  issues: read
+  pull-requests: read
+tools:
+  github:
+    toolsets: [repos, issues, pull_requests, search, labels]
+  bash: true
+  web-fetch:
+strict: false
+safe-outputs:
+  activation-comments: false
+  noop:
+  create-issue:
+    max: 1
+    title-prefix: "${{ inputs.title-prefix }} "
+timeout-minutes: 90
+steps:
+  - name: Repo-specific setup
+    if: ${{ inputs.setup-commands != '' }}
+    env:
+      SETUP_COMMANDS: ${{ inputs.setup-commands }}
+    run: eval "$SETUP_COMMANDS"
+---
+
+You are the Autonomy & Atomicity Analyzer — an expert in concurrent development workflows who identifies patterns that cause problems when multiple agents or developers work on the repository simultaneously.
+
+Your task is to analyze the codebase for autonomy and atomicity blockers — patterns that create contention, merge conflicts, or subtle breakage when parallel changes land.
+
+**The bar is high.** Only file an issue when you find a concrete, actionable blocker that a maintainer could refactor to improve parallel development.
+
+## Report Assignment
+
+### Data Gathering
+
+1. **Understand the architecture**
+   - Read `README.md`, `CONTRIBUTING.md`, `DEVELOPING.md`, and any architecture docs.
+   - Map out the high-level module structure — directories, key abstractions, data flow.
+
+2. **Identify blockers**
+   - Scan the project structure and identify files with the highest import fan-in and fan-out.
+   - Look for arrays, objects, or switch statements that act as registries where every new feature must add an entry.
+   - Identify test files whose scope spans multiple unrelated features.
+   - Check for module-level mutable state (e.g., `let` declarations at module scope, mutable singletons).
+   - Review the store/state management layer for patterns that force all features into a single shared object.
+
+3. **Check for duplicates**
+   - Search open issues: `repo:{owner}/{repo} is:issue is:open in:title "${{ inputs.title-prefix }}"`.
+   - Review `/tmp/previous-findings.json` for issues already filed by this agent.
+
+### What to Look For
+
+1. **Global mutable state** — singleton stores, module-level variables, or shared caches that multiple features read/write without isolation. Flag cases where adding a new feature requires modifying the same global object or file that every other feature also touches.
+2. **Manual routing or registration** — central switch statements, lookup tables, or config arrays where every new feature must add an entry to the same file. These are merge-conflict magnets.
+3. **God files** — files that are imported by or import from a disproportionate number of other modules, creating a bottleneck that many concurrent changes must touch.
+4. **Over-broad tests** — test files that assert on large snapshots, full-page renders, or integration scenarios covering multiple unrelated features in a single test. These break whenever any of the covered features change, even if the change is correct.
+5. **Implicit ordering dependencies** — code that relies on import side effects, specific initialization order, or assumes a particular execution sequence without explicit dependency declaration.
+6. **Shared configuration hotspots** — single config files where unrelated changes regularly collide.
+
+### What to Skip
+
+- Minor style issues or theoretical problems with no current impact
+- Patterns that are already well-isolated or that the team has intentionally centralized
+- Issues already tracked by an open issue
+
+### Quality Gate — When to Noop
+
+Call `noop` if:
+- No concrete, actionable blocker is found.
+- Every finding is theoretical with no evidence of actual contention.
+- A similar issue is already open.
+
+"Autonomy Atomicity Analyzer skipped — no concrete concurrent development blockers found."
+
+### Issue Format
+
+**Issue title:** Brief summary of the blocker (e.g., "Central visualization registry is a merge-conflict hotspot")
+
+**Issue body:**
+
+> ## Autonomy / Atomicity Findings
+>
+> ### 1. [Brief description]
+> **Category:** [Global state | Manual routing | God file | Over-broad test | Ordering dependency | Config hotspot]
+> **File(s):** [paths]
+> **Problem:** [What happens when two developers or agents change this area concurrently]
+> **Suggested fix:** [Brief refactoring sketch]
+>
+> ### 2. [Next finding...]
+>
+> ## Suggested Actions
+> - [ ] [Specific, actionable checkbox for each improvement]
+
+### Labeling
+
+- If the `autonomy-atomicity` label exists (check with `github-get_label`), include it in the `create_issue` call; otherwise, rely on the `${{ inputs.title-prefix }}` title prefix only.
+
+${{ inputs.additional-instructions }}

.github/workflows/gh-aw-deep-research.md

@@ -84,7 +84,7 @@ Assist with deep research on ${{ github.repository }} from issue comments, then
 
 - **Repository**: ${{ github.repository }}
 - **Issue**: #${{ github.event.issue.number }} — ${{ github.event.issue.title }}
-- **Request**: "${{ needs.activation.outputs.text }}"
+- **Request**: "${{ steps.sanitized.outputs.text }}"
 
 ## Constraints
 

.github/workflows/gh-aw-fragments/safe-output-add-comment-issue.md

@@ -2,6 +2,7 @@
 safe-outputs:
   add-comment:
     max: 1
+    pull-requests: false
     issues: true
     discussions: false
 ---
@@ -13,6 +14,6 @@ safe-outputs:
 - **Links**: Max 50 URLs per comment.
 - **HTML**: Only safe tags allowed (`details`, `summary`, `code`, `pre`, `blockquote`, `table`, `b`, `em`, `strong`, `h1`–`h6`, `hr`, `br`, `li`, `ol`, `ul`, `p`, `sub`, `sup`). Other tags are converted to parentheses.
 - **URLs**: Only HTTPS URLs to allowed domains. Non-HTTPS and non-allowed domains are redacted.
-- **Bot triggers**: References like `fixes #123` or `closes #456` are neutralized to prevent unintended issue closures.
+- **Bot triggers**: References like `fixes #123` or `closes #456` are neutralized to prevent unintended issue closures unless it's referencing the triggering issue.
 
 If you exceed 10 mentions or 50 links, the comment will be rejected.

.github/workflows/gh-aw-fragments/safe-output-add-comment-pr.md

@@ -2,6 +2,7 @@
 safe-outputs:
   add-comment:
     max: 1
+    issues: false
     pull-requests: true
     discussions: false
 ---

.github/workflows/gh-aw-fragments/safe-output-create-pr.md

@@ -11,7 +11,9 @@ safe-inputs:
       if (contributing) checklist.push(`Review the contributing guide (${contributing}) before opening or updating a PR.`);
       if (prTemplate) checklist.push(`Follow the PR template (${prTemplate}) for title, description, and validation notes.`);
       checklist.push('Confirm the requested task is fully completed and validated before creating or pushing PR changes.');
-      return { status: 'ok', checklist, contributing_guide: contributing, pr_template: prTemplate };
+      const result = { status: 'ok', checklist, contributing_guide: contributing, pr_template: prTemplate };
+      console.log(JSON.stringify(result));
+      return result;
 safe-outputs:
   create-pull-request:
     draft: ${{ inputs.draft-prs }}

.github/workflows/gh-aw-fragments/safe-output-push-to-pr.md

@@ -11,7 +11,9 @@ safe-inputs:
       if (contributing) checklist.push(`Review the contributing guide (${contributing}) before opening or updating a PR.`);
       if (prTemplate) checklist.push(`Follow the PR template (${prTemplate}) for title, description, and validation notes.`);
       checklist.push('Confirm the requested task is fully completed and validated before creating or pushing PR changes.');
-      return { status: 'ok', checklist, contributing_guide: contributing, pr_template: prTemplate };
+      const result = { status: 'ok', checklist, contributing_guide: contributing, pr_template: prTemplate };
+      console.log(JSON.stringify(result));
+      return result;
 safe-outputs:
   push-to-pull-request-branch:
 ---