Address the open issue set: CI truth, proof gates, scanner precision, toolchain policy (21 issues fixed, 3 filed)

[arena-ai-coding-agent]

Addresses the open issue set of hyperpolymath/hypatia in line with rsr-template-repo and standards, plus items needing immediate attention. One commit (30e6d14, five logical waves), 21 issues fixed/resolved, 3 new issues filed from findings, everything else triaged below.

Note on issue comments: the GitHub integration used here can create issues but is refused issue comment / issue close (HTTP 403 "Resource not accessible by integration"). Per-issue dispositions live in this body instead; Closes #… keywords below will close the resolved set on merge.

Wave 1 — CI truth

• CI never passes --locked, so the committed Cargo.lock constrains nothing #841 — --locked now passed on every test/check job (cargo invocations across tests.yml, ci.yml, verify-proofs.yml, abi-codegen-drift.yml, batch-security-scan).
• cargo test --workspace is red on main: unsatisfiable testcontainers conflict (DEBT-REGISTER CI-1 names the wrong cause) #814 — real cause of red cargo test --workspace is the unsatisfiable testcontainers ^0.28 vs testcontainers-modules ^0.15 pair (not "network egress"); versions made satisfiable and DEBT-REGISTER CI-1's cause attribution corrected.
• Security workflow runs two duplicate scan tiers with different aggregators #847–TruffleHog action is pinned but the scanner image it runs is not (version: latest) #851 — security-policy.yml consolidated to one scan tier with a security-status aggregator gating Fail on critical security findings; TruffleHog Gates A/B (verified-only off + historical scan); audit jobs keep and report their findings; container-scan joins the aggregator; scanner image pinned by explicit tag (latest removed). Decision record + per-step manifest at the top of the workflow.

Wave 2 — runtime safety

• test: RateLimiterTest 'tracks active bots' flakes — the suite shares one app-supervised GenServer whose state a crash silently resets #857 — RateLimiterTest "tracks active bots" flake: tests now own named instances via start_supervised! (no sleeps); the drain crasher (finding.type KeyError on string-keyed maps) cannot take the limiter down (try/rescue/catch on dispatch; check_internal/2 mirrors the full check incl. burst); crash-isolation regression test proves owned stats survive GenServer.whereis(RateLimiter) being killed.
• integration/ compose tier is CI-dead and mounts a fixture directory that does not exist #853 — CI-dead integration/ compose tier deleted.

Wave 3 — proofs

• verify-proofs.yml installs Idris2 to PREFIX=/usr/local but the binary reads --libdir under ~/.idris2 #820 — verify-proofs.yml + abi-codegen-drift.yml: single-prefix Idris2 bootstrap (make install PREFIX="$HOME/.idris2", no sudo), cache key -3, PATH export, measurement step printing idris2 --prefix/--libdir + support-lib layout. The abi repair step is retained with a sequencing comment: delete it only after a green -3 run prints "support installation already complete".
• verification/PROOF-STATUS.adoc is stale: wrong path, wrong LOC, wrong proofs #816 — scripts/check-proof-status.sh (new): PROOF-STATUS rows named in docs must exist; Property identifiers must match. Green on tree ("files named 27, identifiers checked 7, mismatches 0"); mutants killed both directions (renamed identifier → red; doc pointing at nonexistent file → red); proof-status job in verify-proofs.yml.
• docs: AFFIRMATION.adoc overclaims 'zero escape hatches'; proof-debt.md cites a nonexistent script and CI job #831 — scripts/check-trusted-base.sh (new): zero escape hatches outside test/soundness/fixtures/. Tree measured 2026-09-26 (marker files = RuleEngine.idr comments + 6 fixtures; 0 assert_total/postulate/%hint/native_decide/admit in code). Run: "fixture=19 allowed=1 comment=1 debt=0"; mutant killed (believe_me planted in verify/src/PipelineState.idr → DEBT red). docs/proof-debt.adoc counts re-derived (6, obj_magic was missing); AFFIRMATION.adoc claim scoped "outside test/soundness/fixtures/". check-trusted-base job in verify-proofs.yml (5 jobs now: type-check, lake-build, tlc, proof-status, check-trusted-base).

Wave 4 — toolchain & policy

• build: mise.toml provisions banned runtimes (python, denojs) and a Python-only toolchain #832 — mise.toml no longer provisions python/denojs or the Python-only toolchain (pip/black/isort/ruff/pytest, PYTHON* env); language-blockers.yml now enforces LANGUAGE-POLICY (Deno manifests banned; TS/ReScript sources banned — whole-tree, measured 0; banned runtimes cannot silently return to mise.toml) instead of its inverse ("Use Deno instead"). The old TS gate was structurally broken (depth-1 checkout vs git diff HEAD~1) and inverted (it blocked bun.lockb telling you to use Deno). Checks green; mutant (planted python = "latest") caught.
• ci(pins): dtolnay/rust-toolchain@v1 is a mutable tag at 22 sites — decide the pinning mechanism, then apply it uniformly #825 — pinning decision recorded in docs/governance/ACTIONS-PINNING.adoc (linked from README): actions.lock is the pinning mechanism for symbolic refs (option (b)) — no partial SHA sweep. Evidence the lock catches a moved ref is in DEBT-REGISTER CI-1's own runner log ("Lockfile pin … does not match ref"). Residual: one deliberate retag-mutant drill.
• Mirror to Git Forges: 3 of 7 forges broken — Gitea's host variable expands to EMPTY, Disroot/Bitbucket keys rejected #845 — mirror.yml pins standards' mirror-reusable.yml at 2479cf76, past the Gitea empty-host fault (host/fingerprint vars now asserted non-empty and named, SSH host keys fingerprint-verified, per-forge skip notices). New Mirror coverage job reports the denominator (N of 7 configured). Disroot/Bitbucket deploy-key registration remains owner action (legible via skip notices). Residual: verify-a-mirror-landed-by-remote-SHA (AC5) needs per-forge remote read.
• Also: two broken README links fixed (DEBT-REGISTER.md → .adoc; PALIMPSEST.adoc now points at hyperpolymath/standards where the file lives).

Wave 5 — scanner precision & docs

• scanner: RE005 matches '|| true' inside comments; zig_ptr_cast/zig_align_cast flag the mandatory opaque-handle idiom #834 — the comment-matching and line-1 defects, mechanism-level: Zig comment stripping (// incl //////!); scan_content reports real line numbers (sarif region.startLine no longer defaults to 1); inline hypatia:ignore <rule> / hypatia: allow code_safety/<rule> directives honoured per line; ffi/zig/src/main.zig's opaque-handle casts carry reviewed pragmas (cast code unchanged); RE005 strips YAML comments before matching and honours hypatia:ignore RE005 -- <reason>. Both directions fixtured everywhere.
• Scan output is non-deterministic: array ordering and language classification both flip between runs #676 — deterministic language resolution: one shared CrossRepoLearning.primary_language_from_scan_data/1 (declared field → count desc → fixed priority → lexical; total order), used by all three readers. Discriminating test fails on the old Enum.max_by tie-break, passes now. Producer-side array ordering is outside this repo → estate: the verisimdb scan writer is outside hypatia — edges/rows/attacks array ordering must be fixed at ITS emit boundary (from #676) #866.
• secret_detected fires on commented-out lines (critical + revoke_rotate_and_purge) in template .envrc boilerplate #746/Secret rules fire on commented-out placeholders and rate them critical (45 blocking false positives across 73 repos) #748 — secret findings dispositioned: placeholder-shaped values (xxx-runs, ellipses, your-*, changeme, <…>) and whole-line comments demote to medium/report with an explicit reason; an uncommented real-looking value stays critical/revoke_rotate_and_purge. The 45 measured blocking false positives all fall in the demoted class; nothing is silenced. Harvested-corpus carve-out → secret_detected flags harvested reference material: path-based carve-out needed for harvested-registry/ (from #746 sample) #865.
• chore(logtalk): categorized purge of stale Logtalk/SWI-Prolog references (engine retired → Elixir) #636 — category-A purge only: Logtalk-as-current claims removed/annotated from ci.yml header, ROADMAP (3), poc-scanner.sh (2), developer-guide (install + toolchain + diagram + data-flow), admin-guide (6), cicd-guidebook (2), NEURAL-ARCHITECTURE present tense; PROOF-STATUS Logtalk claims annotated with reason (status unchanged). B/C/D untouched: hooks/lib/common.sh, lib/rules migration comments, 6a2 purge records, MUST.contractile (owner-gated → owner-gated: MUST.contractile:79 'Logtalk rule engine must be preserved' contradicts the retired engine (from #636 category C) #864), .audittraining, arcvix paper, system-integration's own residual note.
• chore: grouped licence + metadata debt (PMPL drift, REUSE, CITATION.cff, descriptiles location, rsr_score SSOT bug) #695 — PMPL drift fixed in governance/hypatia-scan/scorecard headers (dogfooding fix-pmpl-drift.sh's own fix); SPDX added to test_helper.exs, test_integration.exs, both check-*.sh, docs/proof-debt.adoc; integration/fixtures/test-repo/src/main.rs stays deliberately headerless (recorded in new .reuse/dep5, which also covers the docs/training corpus); unused LICENSES/AGPL-3.0-or-later.txt removed; CITATION.cff added; .github/TEST_CI_CODEQL_HYPATIA.md deleted per its own "DELETE AFTER VERIFICATION" instruction; mix hypatia.rsr_score resolves its SSOT from real source-tree candidates — the bare command works without --ssot (the old :code.priv_dir/.. path landed inside _build). Stale sub-items confirmed done elsewhere: mise.toml (build: mise.toml provisions banned runtimes (python, denojs) and a Python-only toolchain #832), descriptiles/ migration (6a2/ gone), guix.scm (deleted), License inconsistency: 8 manifests AGPL-3.0-or-later vs LICENSE MPL-2.0 #417 (already closed).

New issues filed (found during this work, not merge blockers)

• owner-gated: MUST.contractile:79 'Logtalk rule engine must be preserved' contradicts the retired engine (from #636 category C) #864 — owner-gated: MUST.contractile:79 "Logtalk rule engine … must be preserved" contradicts the retired engine (chore(logtalk): categorized purge of stale Logtalk/SWI-Prolog references (engine retired → Elixir) #636 category C, doctrine Bump webfactory/ssh-agent from 0.9.0 to 0.9.1 #4: supervised decision).
• secret_detected flags harvested reference material: path-based carve-out needed for harvested-registry/ (from #746 sample) #865 — harvested-registry/ reference material trips secret_detected; path-based carve-out proposal (secret_detected fires on commented-out lines (critical + revoke_rotate_and_purge) in template .envrc boilerplate #746 tail note).
• estate: the verisimdb scan writer is outside hypatia — edges/rows/attacks array ordering must be fixed at ITS emit boundary (from #676) #866 — the verisimdb scans/ writer lives outside hypatia; edges/rows/attacks must be sorted at its emit boundary (the Scan output is non-deterministic: array ordering and language classification both flip between runs #676 producer-side half).

Triage of the remaining open set

#	disposition
358, 359	panic-attack fact-source / higher-order rules — design work, unchanged; no blocker found this pass
361, 363, 366	#333 cohort detector ideas — additive rules; valid backlog
367	M20 SNIF parser port — blocked on its upstream unlock (hypatia#294), untouched
369	code-scanning→dispatch loop RFC — the security-status aggregator pattern from #847 is a building block
421	reusable_workflow_sha_bump_needs_propagation wiring — real; registry+dispatch wiring still missing
447–449	taxonomy/self-model/planner RFCs — out of scope for this pass
463–466	estate ops queues (billing wall, red CI, licence PRs, PR stewardship) — owner-facing, unchanged
470, 471, 473	ruleset audits — ABI-Codegen-Drift is the only active hypatia ruleset (verified); estate-wide Base ruleset audit still open
483	doc + contractile currency — #636/#695/#864 are slices of it
485	rsr-template↔standards divergence audit — needs owner/consistency-plugin access
486	neural-convergence proofs — needs network+Mathlib; out of pass
519	Hypatia check must report on every PR — related to the #847 aggregator design; still open
520	stale standards reusable pins estate-wide — hypatia's own mirror.yml pin bumped to 2479cf76 in this PR; the estate sweep remains (and check-lockfile-drift.sh mode 4 is the detector)
523, 554, 556	scanner deployment/verification ops — unchanged
567	cicd-squabbler feedback channel — design, unchanged
582	ScorecardReconciler scheduling — unchanged
585	ruleset gate-deadlock (structurally-unsatisfiable required checks) — owner/ruleset-admin action; the accept-or-delete ruling applies
605	B-SHAPIN + actions_policy.ex — valid detection backlog
638	allowlist heal-then-wipe oscillation — ops, unchanged
683	CI-health estate failure-class report — ops cadence, unchanged
676	kept open — hypatia side fixed (see above); the producer-side half is #866
845	kept open — Gitea empty-host fault fixed via pin bump; Disroot/Bitbucket key registration (owner) + remote-SHA verification (AC5) remain

Evidence & limits

• All new scripts were run green on the tree and mutant-proven both directions (detailed in each commit message). Scanner rule changes ship with both-directions fixtures.
• No Elixir/Rust toolchain exists in the fix sandbox: mix test / cargo test assertions are written to run in CI on this branch and constitute the test-level acceptance evidence.
• actions.lock kept set-equal to workflow refs (both third-party action tags are v7.0.1/v4.32.0, matching the lock's recorded resolutions).

Closes #814, closes #816, closes #820, closes #825, closes #831, closes #832, closes #834, closes #841, closes #847, closes #848, closes #849, closes #850, closes #851, closes #853, closes #857, closes #636, closes #695, closes #746, closes #748

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