docs(governance): 2026-06-12 checkpoint — dual-STATE reconcile, bot directives, repo-true contractiles

- Root .machine_readable/STATE.a2ml pointer-ized to canonical
  6a2/STATE.a2ml (stale rsr-template S-expr block retired; preserved
  in git history).
- 6a2/STATE.a2ml refreshed to 2026-06-12: recent-work since 2026-04-12
  with PR numbers, blockers (OQ-001 retained, OQ-002 placeholders
  added), maintenance status; converted inline tables to valid TOML.
- 6a2/META.a2ml: valid-TOML ADR array-of-tables; ADR-006 records the
  estate-standardization adoption; last-updated bumped.
- 6a2/anchor/ANCHOR.a2ml: identity placeholders filled (monorepo /
  type-theory coordination), 2026-06-12 realignment entry, template
  residue in semantic-authority-files flagged.
- bot_directives: hypatia.a2ml, gitbot-fleet.a2ml, git-private-farm.a2ml
  added (repo-true facts: thin reusable wrappers, instant-sync presence
  gate absent); README.adoc extended with precedence/scope and trio.
- contractiles: flat Mustfile/Trustfile/Adjustfile/Intentfile rewritten
  with nextgen-typing identity, porting nested must/trust and root
  MUST/TRUST/ADJUST/INTENT contractile content; Dustfile + Bustfile
  added porting nested dust/bust (submodule-era scenarios kept with
  explicit not-applicable status); README updated to flat layout.
- anchors/README.adoc forwarding stub; EXPLAINME.adoc stale katagoria
  claims fixed; docs/wikis/Project-Status.adoc dated status page added.

https://claude.ai/code/session_01GJatEm2TVFSTBEkKXmserJ

Author: claude

.machine_readable/6a2/META.a2ml

@@ -5,28 +5,58 @@
 # Architecture decisions, design rationale, governance.
 
 [metadata]
-version = "0.1.0"
-last-updated = "2026-06-05"
+version = "0.1.1"
+last-updated = "2026-06-12"
 
 [project-info]
 type = "monorepo"  # library | binary | monorepo | service | website
 languages = []             # e.g. ["rust", "zig", "idris2"]
 license = "MPL-2.0"
 author = "Jonathan D.A. Jewell (hyperpolymath)"
 
-[architecture-decisions]
-adrs = [
-  { id = "ADR-001", title = "Coordination monorepo, no compiler code", status = "accepted", date = "2026-04-11",
-    rationale = "nextgen-typing documents relationships and hosts cross-cutting research artefacts. Compiler code lives in the constituent repos (typell, typed-wasm). Follows the nextgen-languages and nextgen-databases precedent." },
-  { id = "ADR-002", title = "TypeLL is open-ended progressive, not capped at 10 levels", status = "accepted", date = "2026-04-11",
-    rationale = "Earlier docs described TypeLL as a '10-level hierarchy'. This is incorrect. TypeLL progressively adds levels as the type theory demands. L1-L10 is the current initial mapping, not a ceiling. The ROADMAP.adoc in typell was updated to reflect this." },
-  { id = "ADR-003", title = "typed-wasm has dual role (ADR-004 in typed-wasm)", status = "accepted", date = "2026-04-11",
-    rationale = "typed-wasm is both the TypeLL WASM safety application AND the aggregate library for AffineScript+Ephapax cross-language binary conventions. Both roles are first-class. See typed-wasm/.machine_readable/6a2/META.a2ml#ADR-004." },
-  { id = "ADR-004", title = "katagoria is the research upstream of typell", status = "accepted", date = "2026-04-11",
-    rationale = "Type theory ideas need an origination space before promotion to production repos. katagoria is that space: Idris2/Lean proofs-of-concept, reading notes, prototype formalizations. The repository was created on 2026-04-11 and is now active in the pipeline." },
-  { id = "ADR-005", title = "Licence migrated from PMPL-1.0-or-later to MPL-2.0", status = "accepted", date = "2026-05-22",
-    rationale = "Repo-wide licence migration to the Palimpsest License (MPL-2.0) (commit 7a84a1d). All SPDX headers now read MPL-2.0; LICENSE body is the Palimpsest variant." },
-]
+# Architecture decisions (array-of-tables; one [[architecture-decisions.adrs]] per ADR)
+
+[[architecture-decisions.adrs]]
+id = "ADR-001"
+title = "Coordination monorepo, no compiler code"
+status = "accepted"
+date = "2026-04-11"
+rationale = "nextgen-typing documents relationships and hosts cross-cutting research artefacts. Compiler code lives in the constituent repos (typell, typed-wasm). Follows the nextgen-languages and nextgen-databases precedent."
+
+[[architecture-decisions.adrs]]
+id = "ADR-002"
+title = "TypeLL is open-ended progressive, not capped at 10 levels"
+status = "accepted"
+date = "2026-04-11"
+rationale = "Earlier docs described TypeLL as a '10-level hierarchy'. This is incorrect. TypeLL progressively adds levels as the type theory demands. L1-L10 is the current initial mapping, not a ceiling. The ROADMAP.adoc in typell was updated to reflect this."
+
+[[architecture-decisions.adrs]]
+id = "ADR-003"
+title = "typed-wasm has dual role (ADR-004 in typed-wasm)"
+status = "accepted"
+date = "2026-04-11"
+rationale = "typed-wasm is both the TypeLL WASM safety application AND the aggregate library for AffineScript+Ephapax cross-language binary conventions. Both roles are first-class. See typed-wasm/.machine_readable/6a2/META.a2ml#ADR-004."
+
+[[architecture-decisions.adrs]]
+id = "ADR-004"
+title = "katagoria is the research upstream of typell"
+status = "accepted"
+date = "2026-04-11"
+rationale = "Type theory ideas need an origination space before promotion to production repos. katagoria is that space: Idris2/Lean proofs-of-concept, reading notes, prototype formalizations. The repository was created on 2026-04-11 and is now active in the pipeline."
+
+[[architecture-decisions.adrs]]
+id = "ADR-005"
+title = "Licence migrated from PMPL-1.0-or-later to MPL-2.0"
+status = "accepted"
+date = "2026-05-22"
+rationale = "Repo-wide licence migration to the Palimpsest License (MPL-2.0) (commit 7a84a1d). All SPDX headers now read MPL-2.0; LICENSE body is the Palimpsest variant."
+
+[[architecture-decisions.adrs]]
+id = "ADR-006"
+title = "Estate standardization layout adopted (estate-standardization-20260607)"
+status = "accepted"
+date = "2026-06-12"
+rationale = "Merged the estate-standardization-20260607 branch: GOVERNANCE.adoc + MAINTAINERS.adoc + .github/CODEOWNERS at root; anchors/ renamed to 6a2/anchor/; agent_instructions/ renamed to bot_directives/; svc/k9/ renamed to self-validating/; nested + root contractiles replaced by flat .machine_readable/contractiles/{Intentfile,Mustfile,Trustfile,Adjustfile,Dustfile,Bustfile}.a2ml; flake.nix removed (Guix is the primary package manager, estate wave decision). Workflow files kept at origin/main's reusable-wrapper versions."
 
 [development-practices]
 build-tool = "just"

.machine_readable/6a2/STATE.a2ml

@@ -6,7 +6,7 @@
 [metadata]
 project = "nextgen-typing"
 version = "0.1.0"
-last-updated = "2026-06-05"
+last-updated = "2026-06-12"
 status = "active"
 
 [project-context]
@@ -17,10 +17,12 @@ Documents and connects: katagoria (research) → typell (kernel) → typed-wasm
 Hosts cross-repo architecture docs, pipeline roadmap, and research artefacts that span projects.
 Does NOT contain compiler code.
 """
-# Reconciled 2026-06-05: the earlier completion=100 was inconsistent with reality.
-# PROOF-STATUS.md records 0 of 7 mandated proofs done (0% proven), and the repo
-# still carries an un-rescoped RSR code scaffold (src/interface/, verification/proofs/).
-# Maturity reflects scaffold/early state, not a finished coordination layer.
+# Reconciled 2026-06-05 (PR #31): the earlier completion=100 was inconsistent with
+# reality. PROOF-STATUS.md records 0 of 7 mandated proofs done (0% proven), and the
+# repo still carries an un-rescoped RSR code scaffold (src/interface/,
+# verification/proofs/). Maturity reflects scaffold/early state, not a finished
+# coordination layer. Recalibration retained at the 2026-06-12 checkpoint: work
+# landed since #31 is CI/governance/docs only — it does not move the scaffold needle.
 completion-percentage = 10
 
 [position]
@@ -31,40 +33,55 @@ maturity = "scaffold"
 milestones = [
   { name = "Repo scaffolded and pushed to GitHub", completion = 100 },
   { name = "README + ROADMAP with pipeline description", completion = 100 },
-  { name = "Machine-readable files populated and state-aligned (STATE/META/ECOSYSTEM)", completion = 80 },
+  { name = "Machine-readable files populated and state-aligned (STATE/META/ECOSYSTEM)", completion = 90 },
   { name = "docs/ARCHITECTURE.adoc cleaned up as pure architecture doc", completion = 100 },
   { name = "docs/PIPELINE.adoc added as machine-readable A2ML pipeline spec", completion = 100 },
   { name = "katagoria repo created and linked from pipeline docs", completion = 100 },
   { name = "ECOSYSTEM.a2ml updated in constituent repos (typell, typed-wasm, affinescript, ephapax, tropical-resource-typing, protocol-squisher)", completion = 100 },
   { name = "Protocol Squisher tropical connection documented", completion = 100 },
 ]
 
+[recent-work]
+# Landed work since 2026-04-12, summarized from git log on origin/main.
+summary = [
+  "2026-04-15..04-18: M5 CI/workflow sweep (contractile.just, blockers), Dependabot security path + auto-merge, contractile 6-verb cleanup (drop lust, add bust/, relocate k9 to svc/), workspace standardization.",
+  "2026-05-12..05-18: CI hardening wave — upload-artifact SHA bump (#1), hypatia-scan token + --exit-zero fix (#2), setup-beam SHA for ubuntu24 (#3), fleet submission no longer fails security gate (#4), stale gen-v-connector recipe removed (#5), k9-validate-action pins (#6), concurrency-cancel guards (#7, #8).",
+  "2026-05-22: licence migrated from PMPL-1.0-or-later to MPL-2.0 repo-wide (commit 7a84a1d).",
+  "2026-05-26..05-30: CI reusable-wrapper rework — hypatia-scan (#10, #25), mirror (#13, #24), secret-scanner (#14, #21), rust-ci (#15, #23), scorecard (#16, #22), reusable SHA repins (#17, #20, #30), fake action-SHA sweep in e2e template stubs (#28); stale SafeDOMExample.res ReScript fixture deleted (#11, #19); tech-debt audit findings recorded in docs/tech-debt-2026-05-26.md (#12, #18); issue templates updated (#26).",
+  "2026-06-06: 6a2 STATE checkpoint — completion/identity reconciled, non-portable paths fixed (#31).",
+  "2026-06-09: README.adoc gains TypeFix Zero (TF0) calibration-calculus section — proposed standalone calibration calculus beside the main chain, design-stage.",
+  "2026-06-12: estate-standardization-20260607 merged — GOVERNANCE.adoc, MAINTAINERS.adoc, .github/CODEOWNERS, 6a2 manifest/README, anchors/ → 6a2/anchor/, agent_instructions/ → bot_directives/, svc/k9/ → self-validating/, flat contractiles, flake.nix removed (Guix primary); codeql cron weekly → monthly; governance checkpoint layer (bot_directives trio, repo-true contractiles, dual-STATE reconciliation).",
+]
+
 [blockers-and-issues]
 issues = [
-  { id = "OQ-001", kind = "open-question", status = "open", raised = "2026-06-05",
-    title = "Identity contradiction — coordination monorepo vs RSR proof scaffold",
-    detail = "Narrative/STATE describe a docs-only coordination monorepo (\"does NOT contain compiler code\"), but src/interface/ + verification/proofs/ carry an un-rescoped RSR code scaffold; reconcile (docs-only ⇒ Tier T5/Exempt, drop scaffold) vs (real proof repo ⇒ re-scope). NOT decided here." },
+  { id = "OQ-001", kind = "open-question", status = "open", raised = "2026-06-05", title = "Identity contradiction — coordination monorepo vs RSR proof scaffold", detail = "Narrative/STATE describe a docs-only coordination monorepo (\"does NOT contain compiler code\"), but src/interface/ + verification/proofs/ carry an un-rescoped RSR code scaffold; reconcile (docs-only ⇒ Tier T5/Exempt, drop scaffold) vs (real proof repo ⇒ re-scope). NOT decided here." },
+  { id = "OQ-002", kind = "template-residue", status = "open", raised = "2026-06-12", title = "Unreplaced template placeholders across community-health files", detail = "{{OWNER}}/{{REPO}}/{{AUTHOR}}/{{SECURITY_EMAIL}}/{{CONDUCT_*}} and friends remain in .github/ community files, self-validating/ k9 templates, and QUICKSTART-MAINTAINER.adoc; .machine_readable/ai/PLACEHOLDERS.adoc is the index. Needs a maintainer fill-in pass (just init or manual)." },
 ]
 
 [critical-next-actions]
 actions = [
+  "Decide OQ-001: docs-only coordination monorepo (drop RSR code scaffold) vs real proof repo (re-scope proofs).",
+  "Replace remaining template placeholders ({{OWNER}}, {{REPO}}, {{SECURITY_EMAIL}}, ...) per .machine_readable/ai/PLACEHOLDERS.adoc.",
   "Track Tropical.thy extensions (linorder instance, tropical matrices, Kleene algebra) in tropical-resource-typing and mirror progress in nextgen-typing docs.",
   "Track and link the arXiv paper draft on speculative tropical session types once published.",
   "Track typed-wasm aggregate ABI convention adoption in AffineScript/Ephapax integration paths as recursive-type support matures.",
   "Run periodic drift scans so README.adoc, docs/ARCHITECTURE.adoc, docs/PIPELINE.adoc, and .machine_readable/6a2/{STATE,META,ECOSYSTEM}.a2ml stay synchronized.",
 ]
 
 [maintenance-status]
-last-run-utc = "2026-06-05T00:00:00Z"
-last-result = "docs-checkpoint"
+last-run-utc = "2026-06-12T00:00:00Z"
+last-result = "governance-checkpoint"
 open-warnings = 0
 open-failures = 0
 
 [recent-activity]
 events = [
   { date = "2026-05-22", kind = "licence", detail = "Migrated licence from PMPL-1.0-or-later to MPL-2.0 across the repo (commit 7a84a1d)." },
   { date = "2026-05-26", kind = "audit", detail = "Recorded estate-wide tech-debt audit findings in docs/tech-debt-2026-05-26.md (combined severity LOW; proof debt = 6 Idris2 believe_me markers in scaffold proof files; licence + docs debt OK)." },
-  { date = "2026-05-30", kind = "ci", detail = "CI reusable-wrapper rework (2026-05-26..2026-05-30): hypatia-scan, scorecard, secret-scanner, rust-ci, and mirror workflows converted to thin wrappers of standards reusables; reusable SHA pins repinned to live merge-commit SHAs (latest commit 4a848fd)." },
+  { date = "2026-05-30", kind = "ci", detail = "CI reusable-wrapper rework (2026-05-26..2026-05-30): hypatia-scan, scorecard, secret-scanner, rust-ci, and mirror workflows converted to thin wrappers of standards reusables; reusable SHA pins repinned to live merge-commit SHAs (commit 4a848fd)." },
+  { date = "2026-06-09", kind = "docs", detail = "README.adoc: TypeFix Zero (TF0) calibration-calculus section added (commits f11cc29..ec3496f)." },
+  { date = "2026-06-12", kind = "governance", detail = "Estate standardization merged (governance docs, bot_directives, self-validating, flat contractiles, flake.nix removal); codeql cron monthly; checkpoint layer: dual STATE reconciled (root pointer-ized to 6a2), bot_directives trio added, contractiles populated with repo-true obligations." },
 ]
 
 [ecosystem]

.machine_readable/6a2/anchor/ANCHOR.a2ml

@@ -4,8 +4,8 @@
 # ANCHOR.a2ml - authoritative anchor for this repository
 
 [metadata]
-version = "1.0.0"
-last-updated = "2026-04-11"
+version = "1.0.1"
+last-updated = "2026-06-12"
 
 [anchor]
 schema = "hyperpolymath.anchor/1"
@@ -20,9 +20,9 @@ purpose = [
 
 [identity]
 project = "nextgen-typing"
-kind = "{{PROJECT_KIND}}"                # language | library | service | tool
+kind = "monorepo"                # coordination monorepo (no compiler code; see META ADR-001)
 one-sentence = "Coordination monorepo for the hyperpolymath type theory pipeline (katagoria → typell → typed-wasm → PanLL)"
-domain = "{{PROJECT_DOMAIN}}"
+domain = "type theory / programming-language research coordination"
 
 [semantic-authority]
 policy = "canonical"
@@ -56,7 +56,21 @@ must-have-anchor = true
 must-have-golden-path = true
 
 [semantic-authority-files]
+# NOTE (2026-06-12): the four paths below are template residue — none of them
+# exist in-tree. Kept verbatim pending maintainer decision (tracked as a
+# proposed issue at the 2026-06-12 governance checkpoint). The real
+# architecture authority files today are docs/ARCHITECTURE.adoc and
+# docs/PIPELINE.adoc.
 language-spec = "SPECIFICATION.md"
 formal-proofs = "docs/proofs/PROOFS.adoc"
 type-theory = "docs/theory/THEORY.adoc"
 algorithms = "docs/theory/ALGORITHMS.adoc"
+
+# Dated realignment entries (most recent last).
+
+[[realignments]]
+date = "2026-06-12"
+what = "Estate standardization + governance checkpoint"
+why = "Adopt the estate-standardization-20260607 layout and refresh machine-readable metadata to current reality"
+evidence = "Merge of origin/estate-standardization-20260607 (workflows kept at main's reusable-wrapper versions); codeql cron monthly cherry-pick; root STATE.a2ml pointer-ized to 6a2/STATE.a2ml; 6a2 STATE/META refreshed to 2026-06-12; bot_directives trio (hypatia, gitbot-fleet, git-private-farm) added; flat contractiles populated with repo-true obligations (content ported from nested must/trust/dust/bust and root *.contractile files)"
+

.machine_readable/STATE.a2ml

@@ -1,27 +1,18 @@
-;; SPDX-License-Identifier: MPL-2.0
-;; Project state — update throughout each session
-(state
-  (metadata
-    (version "1.0.1")
-    (project "rsr-template-repo")
-    (last-updated "2026-04-04"))
-  (project-context
-    (description "RSR Standard Repository Template — baseline for all hyperpolymath projects")
-    (primary-language "Idris2 (ABI) + Zig (FFI)")
-    (status "testing-complete"))
-  (current-position
-    (phase "testing")
-    (completion-percentage 100)
-    (milestone "CRG C - Testing & Benchmarking complete"))
-  (testing-summary
-    (validation-script "scripts/validate-template.sh: PASS (0 errors)")
-    (workflow-tests "tests/workflows/validate_workflows_test.sh: PASS (21/21 workflows)")
-    (integration-tests "test/integration_test.zig: PASS (placeholder template)")
-    (e2e-tests "tests/e2e/template_instantiation_test.sh: READY")
-    (benchmarks "benches/template_bench.sh: PASS (5 suites)")
-    (zig-build "Zig 0.15.2 compatible: PASS"))
-  (critical-next-actions
-    ("Commit test suite"
-     "Push to GitHub"
-     "Verify CI workflows pass"
-     "Document test instantiation patterns")))
+# SPDX-License-Identifier: MPL-2.0
+# Copyright (c) 2026 Jonathan D.A. Jewell (hyperpolymath) <j.d.a.jewell@open.ac.uk>
+#
+# STATE.a2ml — POINTER ONLY. The canonical project state lives in
+# .machine_readable/6a2/STATE.a2ml (single source of truth per the
+# 6a2 invariant "no duplicate files in root directory").
+#
+# This file formerly carried a Guile S-expression state block for
+# "rsr-template-repo" (template residue, last updated 2026-04-04,
+# claiming completion 100). That content was superseded by the
+# reconciled 6a2 STATE (2026-06-05, PR #31) and is preserved in git
+# history (see commit ec3496f and earlier).
+
+[pointer]
+canonical = ".machine_readable/6a2/STATE.a2ml"
+reason = "6a2 directory is authoritative; root duplicate retired 2026-06-12"
+retired-content = "rsr-template-repo S-expr state block (stale template residue)"
+last-updated = "2026-06-12"

.machine_readable/anchors/README.adoc

@@ -1,3 +1,7 @@
 // SPDX-License-Identifier: MPL-2.0
 // Copyright (c) Jonathan D.A. Jewell <j.d.a.jewell@open.ac.uk>
 = anchors Registry
+
+MOVED: the anchor record now lives at `.machine_readable/6a2/anchor/ANCHOR.a2ml`
+(estate-standardization layout, 2026-06-12). This directory remains only as a
+forwarding stub for older references.

.machine_readable/bot_directives/README.adoc

@@ -1,17 +1,35 @@
 // SPDX-License-Identifier: MPL-2.0
 // Copyright (c) Jonathan D.A. Jewell <j.d.a.jewell@open.ac.uk>
-= Agent Instructions
+= Bot Directives
 :toc: preamble
 
-Methodology-aware configuration for AI agents. Read by any AI agent
-(Claude, Gemini, Copilot, etc.) at session start.
+Per-repo directives for automated agents, read at session start by any
+AI agent (Claude, Gemini, Copilot, etc.) and by the automation fleet.
+
+*Precedence:* maintainer > these directives > bot defaults.
+
+*Scope:* applies to the hypatia scanner, the gitbot fleet, and
+`.git-private-farm` propagation, plus the methodology layer for
+interactive agents.
 
 == Files
 
 [cols="1,3"]
 |===
 | File | Purpose
 
+| `hypatia.a2ml`
+| Hypatia security-scanner directives — accepted findings (known
+  false-positives with reasons), prohibited actions, escalation path
+
+| `gitbot-fleet.a2ml`
+| Gitbot fleet roster (rhodibot, echidnabot, sustainabot, glambot,
+  seambot, finishbot), branch policy, never-touch paths, per-bot rules
+
+| `git-private-farm.a2ml`
+| Propagation directives for `hyperpolymath/.git-private-farm`
+  (instant-sync workflow, secret NAME, rotation procedure)
+
 | `methodology.a2ml`
 | Default mode, invariants, ring ceiling, priority weights, convergent budget
 
@@ -27,14 +45,16 @@ Methodology-aware configuration for AI agents. Read by any AI agent
 1. Read `methodology.a2ml` at session start — know mode, invariants, ceiling
 2. Read `coverage.a2ml` — know what was visited last time, what was skipped
 3. Read `debt.a2ml` — know what's outstanding from previous sessions
-4. At session end, update `coverage.a2ml` and `debt.a2ml`
+4. Consult `hypatia.a2ml` / `gitbot-fleet.a2ml` / `git-private-farm.a2ml`
+   before scanner triage, fleet operations, or propagation changes
+5. At session end, update `coverage.a2ml` and `debt.a2ml`
 
 == Relationship to Other Files
 
-* `AGENTIC.a2ml` says WHAT agents can do (permissions, gating)
-* `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)
+* `../6a2/AGENTIC.a2ml` says WHAT agents can do (permissions, gating)
+* `bot_directives/` says HOW agents should work (methodology) and what
+  the automation fleet may do (fleet-specific)
+* `CLAUDE.md` (where present) says how Claude specifically should work
 
 == Reference