chore: rename agent_instructions to bot_directives for spec alignment

hyperpolymath · hyperpolymath · commit a4a32ab397f2 · 2026-06-04T18:55:46.000+01:00
diff --git a/.github/workflows/boj-build.yml b/.github/workflows/boj-build.yml
@@ -7,6 +7,7 @@ on:
 jobs:
   trigger-boj:
     runs-on: ubuntu-latest
+    timeout-minutes: 15
     steps:
       - name: Checkout
         uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
diff --git a/.github/workflows/casket-pages.yml b/.github/workflows/casket-pages.yml
@@ -18,6 +18,7 @@ concurrency:
 jobs:
   build:
     runs-on: ubuntu-latest
+    timeout-minutes: 15
     steps:
       - name: Checkout
         uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
@@ -109,6 +110,7 @@ jobs:
       name: github-pages
       url: ${{ steps.deployment.outputs.page_url }}
     runs-on: ubuntu-latest
+    timeout-minutes: 15
     needs: build
     steps:
       - name: Deploy to GitHub Pages
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -17,6 +17,7 @@ jobs:
   test:
     name: Julia ${{ matrix.julia-version }} - ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
+    timeout-minutes: 15
     strategy:
       fail-fast: false
       matrix:
diff --git a/.github/workflows/governance.yml b/.github/workflows/governance.yml
@@ -32,3 +32,4 @@ permissions:
 jobs:
   governance:
     uses: hyperpolymath/standards/.github/workflows/governance-reusable.yml@861b5e911d9e5dcfb3c0ab3dd2a9a3c8fd0a1613
+    timeout-minutes: 10
diff --git a/.github/workflows/hypatia-scan.yml b/.github/workflows/hypatia-scan.yml
@@ -43,6 +43,7 @@ jobs:
   scan:
     name: Hypatia Neurosymbolic Analysis
     runs-on: ubuntu-latest
+    timeout-minutes: 15
 
     steps:
       - name: Checkout repository
diff --git a/.github/workflows/instant-sync.yml b/.github/workflows/instant-sync.yml
@@ -14,6 +14,7 @@ permissions:
 jobs:
   dispatch:
     runs-on: ubuntu-latest
+    timeout-minutes: 15
     steps:
       - name: Trigger Propagation
         uses: peter-evans/repository-dispatch@28959ce8df70de7be546dd1250a005dd32156697 # v3
diff --git a/.github/workflows/mirror.yml b/.github/workflows/mirror.yml
@@ -13,6 +13,7 @@ permissions:
 jobs:
   mirror-gitlab:
     runs-on: ubuntu-latest
+    timeout-minutes: 15
     if: vars.GITLAB_MIRROR_ENABLED == 'true'
     steps:
       - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
@@ -31,6 +32,7 @@ jobs:
 
   mirror-bitbucket:
     runs-on: ubuntu-latest
+    timeout-minutes: 15
     if: vars.BITBUCKET_MIRROR_ENABLED == 'true'
     steps:
       - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
@@ -49,6 +51,7 @@ jobs:
 
   mirror-codeberg:
     runs-on: ubuntu-latest
+    timeout-minutes: 15
     if: vars.CODEBERG_MIRROR_ENABLED == 'true'
     steps:
       - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
@@ -67,6 +70,7 @@ jobs:
 
   mirror-sourcehut:
     runs-on: ubuntu-latest
+    timeout-minutes: 15
     if: vars.SOURCEHUT_MIRROR_ENABLED == 'true'
     steps:
       - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
@@ -85,6 +89,7 @@ jobs:
 
   mirror-disroot:
     runs-on: ubuntu-latest
+    timeout-minutes: 15
     if: vars.DISROOT_MIRROR_ENABLED == 'true'
     steps:
       - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
@@ -103,6 +108,7 @@ jobs:
 
   mirror-gitea:
     runs-on: ubuntu-latest
+    timeout-minutes: 15
     if: vars.GITEA_MIRROR_ENABLED == 'true'
     steps:
       - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
@@ -121,6 +127,7 @@ jobs:
 
   mirror-radicle:
     runs-on: ubuntu-latest
+    timeout-minutes: 15
     if: vars.RADICLE_MIRROR_ENABLED == 'true'
     steps:
       - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
diff --git a/.github/workflows/scorecard-enforcer.yml b/.github/workflows/scorecard-enforcer.yml
@@ -23,6 +23,7 @@ permissions:
 jobs:
   scorecard:
     runs-on: ubuntu-latest
+    timeout-minutes: 15
     permissions:
       security-events: write
       id-token: write  # For OIDC
@@ -61,6 +62,7 @@ jobs:
   # Check specific high-priority items
   check-critical:
     runs-on: ubuntu-latest
+    timeout-minutes: 15
     steps:
       - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
 
diff --git a/.github/workflows/secret-scanner.yml b/.github/workflows/secret-scanner.yml
@@ -21,6 +21,7 @@ permissions:
 jobs:
   trufflehog:
     runs-on: ubuntu-latest
+    timeout-minutes: 15
     steps:
       - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
         with:
@@ -33,6 +34,7 @@ jobs:
 
   gitleaks:
     runs-on: ubuntu-latest
+    timeout-minutes: 15
     steps:
       - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
         with:
@@ -46,6 +48,7 @@ jobs:
   # Rust-specific: Check for hardcoded crypto values
   rust-secrets:
     runs-on: ubuntu-latest
+    timeout-minutes: 15
     if: hashFiles('**/Cargo.toml') != ''
     steps:
       - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
diff --git a/.machine_readable/6a2/0-AI-MANIFEST.a2ml b/.machine_readable/6a2/0-AI-MANIFEST.a2ml
@@ -0,0 +1,31 @@
+# AI Manifest for 6a2 Directory
+
+## Purpose
+
+This manifest declares the AI-assistant context for the 6a2 machine-readable metadata directory.
+
+## Canonical Locations
+
+The 6 core A2ML files MUST exist in this directory:
+1. AGENTIC.a2ml
+2. ECOSYSTEM.a2ml
+3. META.a2ml
+4. NEUROSYM.a2ml
+5. PLAYBOOK.a2ml
+6. STATE.a2ml
+
+## Invariants
+
+- No duplicate files in root directory
+- Single source of truth: this directory is authoritative
+- No stale metadata
+
+## Protocol
+
+When multiple agents may write to A2ML files concurrently:
+1. Read file and record git-sha-at-read in [provenance] section
+2. Lock by creating .lock-<FILENAME>
+3. Write updated file with new [provenance] metadata
+4. Release by removing lock file
+5. On conflict: re-read and retry if git-sha-at-read does not match HEAD
+
diff --git a/.machine_readable/6a2/README.adoc b/.machine_readable/6a2/README.adoc
@@ -0,0 +1,30 @@
+// SPDX-License-Identifier: MPL-2.0
+// Copyright (c) Jonathan D.A. Jewell <j.d.a.jewell@open.ac.uk>
+# A2ML 6a2 Directory
+
+This directory contains the 6 core A2ML machine-readable metadata files for this repository.
+
+## Files
+
+- `AGENTIC.a2ml` - AI agent operational gating, safety controls
+- `ECOSYSTEM.a2ml` - Project ecosystem position, relationships, explicit boundaries
+- `META.a2ml` - Architecture decisions (ADRs), development practices, design rationale
+- `NEUROSYM.a2ml` - Symbolic semantics, composition algebra
+- `PLAYBOOK.a2ml` - Executable plans, operational runbooks
+- `STATE.a2ml` - Project state, phase, milestones, session history
+
+## Standards Compliance
+
+These files follow the A2ML Format Family specification from:
+https://github.com/hyperpolymath/standards/tree/main/a2ml
+
+## Generation
+
+These files may be generated from .scm source files using transpilation tools.
+Source .scm files should be removed after successful transpilation.
+
+## See Also
+
+- [A2ML Repository Template](https://github.com/hyperpolymath/standards/blob/main/A2ML-REPO-TEMPLATE.adoc)
+- [6A2 Format Family](https://github.com/hyperpolymath/standards#a2ml-format-family-7-formats)
+
diff --git a/.machine_readable/6a2/anchor/0-AI-MANIFEST.a2ml b/.machine_readable/6a2/anchor/0-AI-MANIFEST.a2ml
@@ -0,0 +1,21 @@
+# AI Manifest for Anchor Directory
+
+## Purpose
+
+This manifest declares the AI-assistant context for the anchor machine-readable metadata directory.
+
+## Canonical Locations
+
+ANCHOR.a2ml files MUST exist in this directory.
+
+## Multiple Versions
+
+Unlike other A2ML files, multiple versions of ANCHOR.a2ml with different dates MAY exist.
+Each version represents a specific recalibration point.
+
+## Invariants
+
+- Multiple versions with different dates are permitted
+- No other A2ML files in this directory
+- Single source of truth for anchor documents
+
diff --git a/.machine_readable/6a2/anchor/ANCHOR.a2ml b/.machine_readable/6a2/anchor/ANCHOR.a2ml
diff --git a/.machine_readable/6a2/anchor/README.adoc b/.machine_readable/6a2/anchor/README.adoc
@@ -0,0 +1,25 @@
+// SPDX-License-Identifier: MPL-2.0
+// Copyright (c) Jonathan D.A. Jewell <j.d.a.jewell@open.ac.uk>
+# A2ML Anchor Directory
+
+This directory contains ANCHOR.a2ml files for project recalibration and scope intervention.
+
+## Files
+
+- `ANCHOR.a2ml` - Project recalibration, scope intervention, canonical authority
+
+## Multiple Versions
+
+Unlike other A2ML files, multiple versions of ANCHOR.a2ml with different dates may exist.
+Each version represents a specific recalibration point in the project history.
+
+## Standards Compliance
+
+These files follow the ANCHOR.a2ml specification from:
+https://github.com/hyperpolymath/standards/tree/main/anchor-a2ml
+
+## See Also
+
+- [A2ML Repository Template](https://github.com/hyperpolymath/standards/blob/main/A2ML-REPO-TEMPLATE.adoc)
+- [Anchor A2ML Spec](https://github.com/hyperpolymath/standards/tree/main/anchor-a2ml)
+
diff --git a/.machine_readable/bot_directives/README.adoc b/.machine_readable/bot_directives/README.adoc
@@ -1,5 +1,5 @@
 // SPDX-License-Identifier: MPL-2.0
-// Copyright (c) 2026 Jonathan D.A. Jewell (hyperpolymath) <j.d.a.jewell@open.ac.uk>
+// Copyright (c) Jonathan D.A. Jewell <j.d.a.jewell@open.ac.uk>
 = Agent Instructions
 :toc: preamble
 
@@ -32,7 +32,7 @@ Methodology-aware configuration for AI agents. Read by any AI agent
 == Relationship to Other Files
 
 * `AGENTIC.a2ml` says WHAT agents can do (permissions, gating)
-* `agent_instructions/` says HOW agents should work (methodology)
+* `bot_directives/` says HOW agents should work (methodology)
 * `bot_directives/` says what the gitbot-fleet does (fleet-specific)
 * `CLAUDE.md` says how Claude specifically should work (Claude-specific)
 
diff --git a/.machine_readable/bot_directives/coverage.a2ml b/.machine_readable/bot_directives/coverage.a2ml
diff --git a/.machine_readable/bot_directives/debt.a2ml b/.machine_readable/bot_directives/debt.a2ml
diff --git a/.machine_readable/bot_directives/methodology.a2ml b/.machine_readable/bot_directives/methodology.a2ml
diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
@@ -1,3 +1,7 @@
+<!--
+SPDX-License-Identifier: MPL-2.0
+Copyright (c) Jonathan D.A. Jewell <j.d.a.jewell@open.ac.uk>
+-->
 # Code of Conduct
 
 
diff --git a/CONTRIBUTING.adoc b/CONTRIBUTING.adoc
@@ -1,3 +1,5 @@
+// SPDX-License-Identifier: MPL-2.0
+// Copyright (c) Jonathan D.A. Jewell <j.d.a.jewell@open.ac.uk>
 = Contributing to AcceleratorGate.jl
 :toc: preamble
 :icons: font
diff --git a/EXPLAINME.adoc b/EXPLAINME.adoc
@@ -1,4 +1,5 @@
 // SPDX-License-Identifier: MPL-2.0
+// Copyright (c) Jonathan D.A. Jewell <j.d.a.jewell@open.ac.uk>
 = AcceleratorGate.jl — Show Me The Receipts
 Jonathan D.A. Jewell <j.d.a.jewell@open.ac.uk>
 :toc:
diff --git a/QUICKSTART-DEV.adoc b/QUICKSTART-DEV.adoc
@@ -1,3 +1,5 @@
+// SPDX-License-Identifier: MPL-2.0
+// Copyright (c) Jonathan D.A. Jewell <j.d.a.jewell@open.ac.uk>
 = Acceleratorgate.Jl — Developer Quickstart
 :toc: preamble
 
diff --git a/QUICKSTART-MAINTAINER.adoc b/QUICKSTART-MAINTAINER.adoc
@@ -1,3 +1,5 @@
+// SPDX-License-Identifier: MPL-2.0
+// Copyright (c) Jonathan D.A. Jewell <j.d.a.jewell@open.ac.uk>
 = Acceleratorgate.Jl — Maintainer Quickstart
 :toc: preamble
 
diff --git a/QUICKSTART-USER.adoc b/QUICKSTART-USER.adoc
@@ -1,3 +1,5 @@
+// SPDX-License-Identifier: MPL-2.0
+// Copyright (c) Jonathan D.A. Jewell <j.d.a.jewell@open.ac.uk>
 = Acceleratorgate.Jl — User Quickstart
 :toc: preamble
 
diff --git a/SECURITY.md b/SECURITY.md
@@ -1,4 +1,7 @@
-<!-- SPDX-License-Identifier: MPL-2.0 -->
+<!--
+SPDX-License-Identifier: MPL-2.0
+Copyright (c) Jonathan D.A. Jewell <j.d.a.jewell@open.ac.uk>
+-->
 # Security Policy
 
 ## Reporting a Vulnerability
diff --git a/TEST-NEEDS.md b/TEST-NEEDS.md
@@ -1,3 +1,7 @@
+<!--
+SPDX-License-Identifier: MPL-2.0
+Copyright (c) Jonathan D.A. Jewell <j.d.a.jewell@open.ac.uk>
+-->
 # TEST-NEEDS: AcceleratorGate.jl
 
 ## CRG Grade: C — ACHIEVED 2026-04-04
diff --git a/TOPOLOGY.md b/TOPOLOGY.md
@@ -1,4 +1,7 @@
-<!-- SPDX-License-Identifier: MPL-2.0 -->
+<!--
+SPDX-License-Identifier: MPL-2.0
+Copyright (c) Jonathan D.A. Jewell <j.d.a.jewell@open.ac.uk>
+-->
 <!-- Copyright (c) 2026 Jonathan D.A. Jewell (hyperpolymath) <j.d.a.jewell@open.ac.uk> -->
 
 # TOPOLOGY.md — AcceleratorGate.jl
diff --git a/docs/accessibility/README.adoc b/docs/accessibility/README.adoc
@@ -1,4 +1,5 @@
 // SPDX-License-Identifier: MPL-2.0
+// Copyright (c) Jonathan D.A. Jewell <j.d.a.jewell@open.ac.uk>
 = Burble Accessibility
 :toc: auto
 :icons: font
diff --git a/docs/compliance/ACCESSIBILITY.adoc b/docs/compliance/ACCESSIBILITY.adoc
@@ -1,3 +1,5 @@
+// SPDX-License-Identifier: MPL-2.0
+// Copyright (c) Jonathan D.A. Jewell <j.d.a.jewell@open.ac.uk>
 = Accessibility Compliance
 Status: Partial
 Target: WCAG 2.1 AA
