Claude/post phase 1 1 cleanup#41
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The previous body referenced undefined symbols (download_dir,
do_ingest/2) and used invalid struct literal syntax
(%__MODULE__{...}). The module is on the v1 critical path at step 3
(Phase 1.3) — after the FHI parser — so a real implementation is
premature, but the broken code was a foot-gun: if anyone enabled
:etma_handler, :auto_ingest the supervision tree would fail with
opaque compile-time errors instead of an actionable message.
This change:
- Removes the broken init/1 and handle_call/3 bodies
- Adds a compiling init/1 that logs a clear "not implemented (Phase
1.3)" error and stops with {:stop, :not_implemented}
- Exposes the three module constants (filename_pattern,
document_extensions, code_extensions) as zero-arity functions so
callers and tests can reference them without duplicating regex
literals
- Updates BouncerTest to use the exposed constants and adds a smoke
test for the new init/1 contract
No behaviour change in the default configuration (auto_ingest is off).
Removed:
- CHANGELOG.md (content-identical to CHANGELOG.adoc; project uses
Asciidoctor for the canonical changelog)
- CODE_OF_CONDUCT.md (short stub; CODE_OF_CONDUCT.adoc has the full
Contributor Covenant)
- MAINTAINERS.md (placeholder with "TBD" entries; MAINTAINERS.adoc
has the real list)
- ABI-FFI-README.md (unfilled template — still contained literal
{{PROJECT}} placeholder, never adapted to this repo)
- Containerfile.simple (unused; Containerfile is the dev/base variant,
Containerfile.hardened the production one)
- well-known-template.tar.gz + well-known-template/ (template
scaffolding for setting up a .well-known directory — this repo
already has its own populated .well-known/; the scaffolding belongs
in a separate template repository)
- schemas/config.cue (CUE is prohibited by the language policy; the
schema was unreferenced)
Updated references:
- CONTRIBUTING.md, GOVERNANCE.adoc, SECURITY.md, CODE_OF_CONDUCT.adoc,
QUICKSTART-MAINTAINER.adoc — point at the .adoc replacements
- 0-AI-MANIFEST.a2ml — drop Containerfile.simple from the container
list
- tests/fuzz/placeholder.txt → test/fuzz/.gitkeep (Elixir convention is
the singular form `test/`; the fuzz subdir is a placeholder for
future property/fuzz suites)
- licenses/{MPL-2.0-NL,PALIMPSEST-EN,PALIMPSEST-NL}.txt → LICENSES/translations/
(case-collision on case-insensitive filesystems; SPDX/REUSE
convention is the uppercase LICENSES/ directory)
- configs/config.ncl → docs/examples/nickel-config-example.ncl
(the file is a generic Nickel sample for "my-app", not project
config; it belongs as a documentation example)
- Update CONTRIBUTING.md and TEST-NEEDS.md to point at the new paths
The docs/ tree was a flat dump and several long-form documents were
camped at the repo root. Reorganised into named subgroups so a human
or agent can find things by intent.
New structure under docs/:
- architecture/ — already existed; unchanged
- ai/ — LLM briefings (warmup-dev.md, warmup-user.md)
- examples/ — illustrative examples (forensics-report,
nickel-config-example)
- operations/ — runbooks & operational concerns (failure-modes,
reversibility)
- research/ — background & rationale (palimpsest, competitors,
ideas, citations)
- sessions/ — STATE.scm session checkpoints
- specs/ — protocol & format specs (fhi-schema, integrity)
- status/ — live status reports (test-needs, proof-needs,
seams-review)
Moves out of root → docs/{group}/<kebab-case-name>:
- llm-warmup-dev.md → docs/ai/warmup-dev.md
- llm-warmup-user.md → docs/ai/warmup-user.md
- PALIMPSEST.adoc → docs/research/palimpsest.adoc
- REVERSIBILITY.md → docs/operations/reversibility.md
- TEST-NEEDS.md → docs/status/test-needs.md
- PROOF-NEEDS.md → docs/status/proof-needs.md
- SEAMS_REVIEW.adoc → docs/status/seams-review.adoc
Moves within docs/:
- docs/CITATIONS.adoc → docs/research/citations.adoc
- docs/COMPETITORS.md → docs/research/competitors.md
- docs/IDEAS.md → docs/research/ideas.md
- docs/FAILURE-MODES.md → docs/operations/failure-modes.md
- docs/FHI-SCHEMA.adoc → docs/specs/fhi-schema.adoc
- docs/INTEGRITY.adoc → docs/specs/integrity.adoc
- docs/FORENSICS-REPORT-EXAMPLE.adoc → docs/examples/forensics-report.adoc
- docs/SESSION-2026-01-06.scm → docs/sessions/2026-01-06.scm
ROADMAP.adoc and TOPOLOGY.md stay at the root because they are the
two highest-traffic "where are we / what's next" files.
Cross-references updated:
- ROADMAP.adoc, Justfile, 0-AI-MANIFEST.a2ml — point at new paths
- docs/specs/integrity.adoc — peer-link adjusted (FHI-SCHEMA.adoc →
fhi-schema.adoc; architecture link prefixed with ../)
…L→MPL migration GitHub config: - Remove root FUNDING.yml. .github/FUNDING.yml is the canonical GitHub-recognised path and was already populated with real handles; the root copy was an empty stub from earlier scaffolding. Scripts: - build-affine.sh → experiments/affine-frontend/build.sh, since AffineScript is post-v1 experimental work. Path-handling updated: walk up two levels to project root for priv/static/wasm, look for main.affine next to the script. Justfile updated accordingly. - setup.sh and setup.ps1 stay at the repo root because their one-line installer URLs are part of the public contract (curl ...raw.githubusercontent.com/.../main/setup.sh). License migration aftermath (the PMPL-1.0 → MPL-2.0 migration in 50863bf was incomplete): - Update 4 stale SPDX-License-Identifier headers from PMPL-1.0 to MPL-2.0: 3 workflows (codeql, secret-scanner, scorecard) and lib/etma_handler/proven/safe_state_machine.ex. - README.adoc shield: PMPL-1.0 → MPL-2.0. - Rewrite docs/research/palimpsest.adoc to describe the post-migration state (Palimpsest is MPL-2.0 in SPDX terms) and link to LICENSE / NOTICE / LICENSES/translations/. - Update k9 setup-repo example to reference the Palimpsest (MPL-2.0) license. - Delete LICENSES/PMPL-1.0.txt and LICENSES/PMPL-1.0-or-later.txt; the binding text is now LICENSES/MPL-2.0.txt and the standard text is in the root LICENSE.
Two new entry-point documents: - docs/README.adoc — a single index that lets a reader (human or AI) start from "what I want to do" and arrive at the right file. Maps goals (run the app, set up dev, audit tests, …) to documents, and explains the docs/ taxonomy by directory. - RSR_COMPLIANCE.adoc — this project's compliance state against the Rhodium Standard Repository spec. Replaces the misnomer RSR_OUTLINE.adoc, which was actually a copy of the upstream RSR template's own README. Tracks: required files, language policy, build system, container strategy, and the two intentional deviations (lib/ + test/ are Elixir conventions; STATE lives in .machine_readable/6a2/STATE.a2ml). - RSR_OUTLINE.adoc → docs/research/rsr-template.adoc — the template-describes-itself content lives in research/ as reference material rather than masquerading as this project's compliance document. README.adoc updates: - Reflect that the CubDB Repo is now real (Phase 1.1 landed) when describing the Status section. - Add pointers to docs/README.adoc and RSR_COMPLIANCE.adoc. - Fix broken link (CONTRIBUTING.adoc → CONTRIBUTING.md). - Rewrite License section to use the post-migration wording (Palimpsest License (MPL-2.0)) and link to LICENSE / NOTICE / docs/research/palimpsest.adoc. - Remove duplicate "Architecture" section that appeared at EOF. - Tech-stack table: Elixir 1.14+/OTP 25+ → Elixir 1.18+/OTP 25 (matches .tool-versions). .machine_readable/agent_instructions/debt.a2ml — update commented-out debt entry to reference the new path.
CHANGELOG.adoc — full rewrite: - Convert from mixed Markdown/AsciiDoc syntax to clean AsciiDoc. - Fix bogus SPDX header (was "MIT" in HTML comments; file is MPL-2.0). - Drop the fictional [2.0.0] / [1.0.0] historical entries — this project is 0.1.0-alpha scaffold with no formal release ever cut. - Move the "rewrote from Java" framing to a single "Earlier history" section that's honest about origin. - Populate [Unreleased] with the actual recent changes: Phase 1.1 Repo, repo reorganisation, Bouncer fix, PMPL→MPL migration finish, doc taxonomy. TOPOLOGY.md — refresh dashboard: - Repo (CubDB): 0% → 70% (Phase 1.1 landed: 280 LOC + 237 LOC tests). - Bouncer: 10% → 20% (init/1 fixed to compile cleanly). - ApiController /health: 30% → 70% (uses Repo.cubdb/0; the stale "Repo.get/1 does not exist" note is no longer true). - ExUnit suite: 4 files → 5 files; 20% → 30%. - Overall: 25-30% → 30-35%. - v1 critical path diagram: mark step 1 done; add note that step 2 is waiting on real .fhi fixtures. - "Last updated" date bumped. .machine_readable/6a2/STATE.a2ml — refresh: - last-updated, version, completion %, phase string. - Add [layout] section pointing at the new entry-point documents. - Add [v1-critical-path] section so agents can read step status without parsing TOPOLOGY's ASCII bars. 0-AI-MANIFEST.a2ml — final Nix mop-up: - packaging list still referenced flake.nix as Nix fallback; replaced with mix.exs (Mix release) to match guix.scm primary cascade.
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The wiki at https://github.com/hyperpolymath/tma-mark2/wiki was a single default "Welcome" page. Populated it with a complete navigation layer that mirrors the in-repo documentation: - Home — landing page, quick-link table, repo metadata - _Sidebar, _Footer — global navigation chrome - Getting-Started — install / run / just recipes - Roadmap-and-Status — v1 critical path, dashboard summary - Architecture — diagram + links to docs/architecture/ - Development — language policy, daily loops, testing philosophy - AI-Agent-Briefing — entry points for LLM agents - Documentation-Index — mirrors docs/README.adoc - RSR-Compliance — summary of RSR_COMPLIANCE.adoc - FHI-Format — pointer to docs/specs/fhi-schema.adoc - Governance — pointer to GOVERNANCE.adoc and the MAA/RMR/RMO trio - License — Palimpsest (MPL-2.0) summary The pages live under docs/wiki/ as the canonical source of truth. The wiki itself is a separate Git repository (tma-mark2.wiki.git) outside this repo's signing/CI scope, so it must be synced manually — docs/wiki/README.md documents the procedure (three-line shell snippet) and the optional GitHub Action that can automate it. Every wiki page is a navigation layer only: authoritative content remains in the repository (docs/, README.adoc, TOPOLOGY.md, …) and the wiki pages link back rather than duplicating. docs/README.adoc — add a row for docs/wiki/ so the staging area is discoverable from the main documentation index.
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…ample Captures the state of PR #41's CI at session end so the open red checks have context for the next reader. Files: - docs/examples/nickel-config-example.ncl — add SPDX header. Direct consequence of the configs/ → docs/examples/ move; Hypatia bot flagged the missing header on PR #41. - docs/status/ci-state.md (new) — full snapshot: check-by-check disposition, Hypatia bot findings categorised (mine vs pre-existing), and a punchlist for taking CI to green that lives outside the scope of this PR. - TOPOLOGY.md — CI workflows row: 60% → 50% with a pointer to docs/status/ci-state.md (was previously hand-waving "most are governance, not value-adding"; now points at the actual red list). - CHANGELOG.adoc — record the SPDX fix in [Unreleased]. - .machine_readable/6a2/STATE.a2ml — add [open-prs] and [ci-state] sections so agents can read the PR situation without parsing TOPOLOGY's ASCII or the CHANGELOG.
Owner
Author
Summary of this PR9 commits, ~110 files, net −1500 / +1100. Repo tidy + docs taxonomy + GitHub wiki staging, plus three opportunistic fixes done in passing. What landed
CI status5 red checks. One was mine and is fixed (Hypatia flagged a missing SPDX on the moved Nickel file — fixed in The other four are pre-existing and out of scope for this PR — captured in
Hypatia findings98 total. 3 critical, 58 high, 37 medium. Only one was mine (the SPDX, now fixed). The rest pre-date this PR — see ci-state.md for the breakdown. WikiWiki content is staged at Session ending. PR is ready for human review; happy to pick up after merge or feedback. Generated by Claude Code |
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…no fmt/lint scope Three independent CI fixes to unblock #41 (post-phase-1-1-cleanup): 1. **actions/cache deprecated SHA** — bump `0c45773b...4f9` → `0057852b...830` (current v4 tag). The old SHA was hard-failed by GitHub's automatic deprecation policy. Two workflows affected: `casket-pages.yml` and `elixir-ci.yml`. 2. **`.hypatia-ignore`** — exempt `examples/SafeDOMExample.res` from the `cicd_rules/banned_language_file` rule. Scheduled for ReScript→AffineScript migration in affinescript#57; until then, exempting unblocks unrelated PRs (same pattern just landed on the-nash-equilibrium#43 + universal-chat-extractor#68). 3. **`deno.json`** — scope `deno fmt` to `assets/js/` so it doesn't require formatting of every markdown / YAML / issue-template file in the repo; exclude `assets/vendor/` from both lint+fmt because `topbar.js` is third-party. Applied formatting to `assets/js/app.js` (let → const, spaces around braces, trailing semicolons). Closes the three CI blockers on #41 — no source-logic changes. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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"scorecard_check": "SAST"
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"file": ".",
"action": "delete_remote_branches",
"rule_module": "git_state",
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}
]Powered by Hypatia Neurosymbolic CI/CD Intelligence |
…/0.22) The lock previously pinned finch 0.20.0 while req 0.5.18 requires finch ~> 0.21.0 or ~> 0.22.0, so mix deps.get exit-1'd in CI. Regenerated locally (mix deps.unlock --all && mix deps.get) bumps finch to 0.22.0 — req 0.5.18's preferred dependency. No mix.exs changes; req ~> 0.5 still resolves to 0.5.18 as before. Refs PR #41 — Elixir CI Install deps step.
🔍 Hypatia Security ScanFindings: 97 issues detected
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{
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]Powered by Hypatia Neurosymbolic CI/CD Intelligence |
The estate-wide Deno CI logic now lives in hyperpolymath/standards/.github/workflows/deno-ci-reusable.yml (filed 2026-05-26 as standards#168). The reusable fixes three bugs that bit this repo in CI: * deno test ran unconditionally and failed 'No test modules found' * deno lint / deno fmt ran unconditionally and failed 'No target files' * no top-level permissions: tripping the workflow security linter Drops the legacy 'npx rescript' step (banned in new code 2026-04-30). Pinned to the #168 head SHA. After #168 merges to main, the pin can be flipped to @main as part of estate cleanup (governance.yml already follows this pattern). Refs hyperpolymath/standards#168.
Owner
Author
|
Added a CI follow-up commit ( The reusable fixes the three bugs the legacy template was hitting estate-wide:
Also drops the banned |
🔍 Hypatia Security ScanFindings: 97 issues detected
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]Powered by Hypatia Neurosymbolic CI/CD Intelligence |
CI was using Elixir 1.15 but mix.exs declares 'elixir: "~> 1.17"',
so mix compile exit-1'd at the very first step:
** (Mix) You're trying to run :etma_handler on Elixir v1.15.8
but it has declared in its mix.exs file it supports only
Elixir ~> 1.17
OTP 26 (already pinned) is compatible with Elixir 1.17. No mix.exs
or .tool-versions change needed — the constraint there is the
source-of-truth; this aligns CI with it.
Refs PR #41 Elixir CI / test step.
🔍 Hypatia Security ScanFindings: 97 issues detected
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"reason": "Action hyperpolymath/standards/.github/workflows/governance-reusable.yml@main needs attention",
"type": "unpinned_action",
"file": "governance.yml",
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"rule_module": "workflow_audit",
"severity": "high"
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{
"reason": "Code.eval_* -- arbitrary code execution risk (1 occurrences, CWE-94)",
"type": "elixir_code_eval",
"file": "/home/runner/work/tma-mark2/tma-mark2/lib/etma_handler/logic/calculator.ex",
"action": "flag",
"rule_module": "code_safety",
"severity": "critical"
},
{
"reason": "binary_to_term without :safe option -- deserialization attack (1 occurrences, CWE-502)",
"type": "elixir_send_unsanitised",
"file": "/home/runner/work/tma-mark2/tma-mark2/lib/etma_handler/settings.ex",
"action": "flag",
"rule_module": "code_safety",
"severity": "high"
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{
"reason": "binary_to_term without :safe option -- deserialization attack (2 occurrences, CWE-502)",
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"file": "/home/runner/work/tma-mark2/tma-mark2/lib/etma_handler/crypto/encrypted_storage.ex",
"action": "flag",
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"severity": "high"
},
{
"reason": "expect() in hot path (21 occurrences, CWE-754)",
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"file": "/home/runner/work/tma-mark2/tma-mark2/native/tma_crypto/src/lib.rs",
"action": "flag",
"rule_module": "code_safety",
"severity": "medium"
},
{
"reason": "Download-and-execute pattern (curl|wget pipe to shell) -- verify integrity before execution (4 occurrences, CWE-494)",
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"file": "/home/runner/work/tma-mark2/tma-mark2/setup.sh",
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"severity": "high"
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"line": 36,
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"type": "secret_detected",
"file": "/home/runner/work/tma-mark2/tma-mark2/lib/etma_handler/crypto/encrypted_storage.ex",
"action": "revoke_rotate_and_purge",
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"line": 266,
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"type": "secret_detected",
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"file": "/home/runner/work/tma-mark2/tma-mark2",
"action": "auto_fix",
"rule_module": "scorecard",
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"remediation": "Add CodeQL or equivalent SAST workflow.",
"scorecard_check": "SAST"
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{
"reason": "Repository has 2 non-main remote branch(es). Policy: single main branch only.",
"type": "GS007",
"file": ".",
"action": "delete_remote_branches",
"rule_module": "git_state",
"severity": "medium"
}
]Powered by Hypatia Neurosymbolic CI/CD Intelligence |
…t fail strict-mode build
mix compile --warnings-as-errors applies to whatever is being
compiled — including transitive dependencies. CI was failing on
upstream warnings we don't own:
* rustler's lib/mix/tasks/rustler.new.ex:224 uses :json.decode/1
(added to the Erlang stdlib in OTP 27 / Elixir 1.18)
* use Bitwise deprecated in favour of import Bitwise
* unused 'files' / 'opts' vars in a transitive zip-handling dep
Splitting into two steps:
1. mix deps.compile — compile deps without strict mode
2. mix compile --warnings-as-errors — strict only on our code
Project's own modules still gated by --warnings-as-errors, so the
hygiene we want for our code stays enforced.
Refs PR #41 Elixir CI / Compile step.
🔍 Hypatia Security ScanFindings: 29 issues detected
View findings[
{
"reason": "Action hyperpolymath/standards/.github/workflows/governance-reusable.yml@main needs attention",
"type": "unpinned_action",
"file": "governance.yml",
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"file": ".",
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"rule_module": "git_state",
"severity": "medium"
}
]Powered by Hypatia Neurosymbolic CI/CD Intelligence |
Conflict resolution: keep main's wrapper conversion to standards#174 elixir-ci-reusable but preserve the elixir 1.17 input (mix.exs requires ~> 1.17, not 1.15).
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