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fix(install): bundle installs for compile-only targets pass audit; skip Codex Markdown agents (#3705, #3706) - #3717
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Local bundle install copies packed files without a primitive renderer, so a plugin-native Markdown agent landed unchanged in .codex/agents/*.toml, which Codex cannot load and apm audit reports as a TOMLDecodeError. Treat codex_agent like gemini_command in the bundle layout owner: the file is skipped and one [!] warning names each skipped agent. Targets that deploy Markdown agents natively are unchanged. The bundle layout guard now witnesses the unsupported-format set, with a bypass mutation. Co-authored-by: Copilot App <223556219+Copilot@users.noreply.github.com>
…3705) For targets without native instructions (Codex, Gemini, OpenCode) a local bundle stages its instructions under apm_modules/<slug>/.apm/instructions/ for apm compile. Those staging paths were recorded in local_deployed_files, so apm audit --ci reported them as missing/unresolved deployed files and a clean bundle install could never pass audit. integrate_local_bundle now returns staged files apart from deployed files; the ledger owner records them in a new local_staged_files lockfile field (retiring any pre-#3705 staging claims on reinstall), discovery proves compile staging roots through LockFile.local_staging_slugs, declarative installs carry the record forward, and apm prune retires it with the staging root. Old lockfiles stay readable and keep compiling. New owner record and guard install-deployment-bundle-compile-staging with a MutationCase. apm-spec-waiver: local_staged_files is an implementation-level lockfile extension (schemas allow additional properties); bundle staging is outside the OpenAPM v0.1 surface, so no new req anchor Co-authored-by: Copilot App <223556219+Copilot@users.noreply.github.com>
Daniel Meppiel (danielmeppiel)
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Co-authored-by: Copilot App <223556219+Copilot@users.noreply.github.com>
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🟡 Changes recommended
Legacy bundle reinstalls can leave stale deployment claims that fail CI audits, while pruning absent staging directories leaves records that can incorrectly authorize later compilation.
2 open issues
What changed in this PR
This PR addresses #3705 and #3706 by separating bundle compilation inputs from deployed artifacts and preventing Markdown agents from being installed as invalid Codex TOML files.
Changes:
- Adds
local_staged_filestracking across bundle installation, compilation discovery, lockfile persistence, and pruning. - Skips bundled Codex agents with a warning per file.
- Adds lifecycle tests, architecture guards, and documentation for the new behavior.
| File | Description |
|---|---|
tests/unit/scripts/test_architecture_runner.py |
Registers the staging guard in expected results. |
tests/unit/install/test_install_local_bundle.py |
Tests Codex agent skipping and warnings. |
tests/unit/install/test_install_local_bundle_issue1207.py |
Separates staging assertions from deployment claims. |
tests/unit/deps/test_lockfile_local_staging.py |
Tests staging persistence, migration, and retirement. |
tests/integration/test_local_bundle_compile_only_targets_lifecycle.py |
Covers bundle install, audit, compile, and prune. |
tests/integration/test_install_local_bundle_e2e.py |
Updates Codex expectations to exclude agents. |
tests/integration/test_architecture_owner_rule_mutations.py |
Tests detection of staging-owner bypasses. |
tests/integration/test_architecture_confirmed_bypass_mutations.py |
Guards against copying Markdown into Codex TOML. |
src/apm_cli/primitives/discovery.py |
Uses the lockfile owner to identify staging roots. |
src/apm_cli/install/services.py |
Reports staged files separately from deployed files. |
src/apm_cli/install/phases/lockfile.py |
Preserves staging records during declarative installs. |
src/apm_cli/install/manifest_reconcile.py |
Includes staged files in cleanup protection. |
src/apm_cli/install/local_bundle_paths.py |
Marks Codex agent rendering as unsupported for bundles. |
src/apm_cli/install/local_bundle_handler.py |
Persists staging results and includes them in summaries. |
src/apm_cli/deps/lockfile.py |
Adds staging serialization, discovery, and retirement. |
src/apm_cli/core/deployment_ledger.py |
Separates staging records from deployment ownership. |
src/apm_cli/commands/uninstall/lockfile_state.py |
Recognizes staging as persisted lockfile state. |
src/apm_cli/commands/prune.py |
Retires records for removed staging roots. |
scripts/architecture_linter/diagnostics.py |
Maps the new guard to its architecture category. |
scripts/architecture_linter/checks/marketplace_package_and_registration.py |
Guards the unsupported bundle format set. |
scripts/architecture_linter/checks/install_deployment_analyzers.py |
Registers the compile-staging rule. |
scripts/architecture_linter/checks/install_bundle_compile_staging.py |
Enforces centralized staging ownership and routing. |
packages/apm-guide/.apm/skills/apm-usage/commands.md |
Documents staging and unsupported bundle formats. |
docs/src/content/docs/reference/lockfile-spec.md |
Documents local_staged_files. |
docs/src/content/docs/consumer/deploy-a-bundle.md |
Explains compilation staging and skipped formats. |
CHANGELOG.md |
Records both bundle-install fixes. |
.apm/architecture/owners/install-deployment.json |
Declares the canonical compile-staging owner. |
Review effort: Balanced
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…ning count (#3717) Rewrite a bundle install's lockfile into the pre-#3705 shape (staging as a local-bundle deployment claim), prove audit --ci fails on it, then show a bundle reinstall moves the rows to local_staged_files and compile plus audit --ci pass. Pin the Codex agent case to exactly one [!] skip warning per skipped agent. Co-authored-by: Copilot App <223556219+Copilot@users.noreply.github.com>
integrate_local_bundle no longer hashes staged instructions or returns staged_file_hashes: no caller read them (staging integrity binding is a follow-up). The dry-run and real deploy paths now share one claim and hash point, keeping the function within its complexity budget. LockFile.local_staging_slugs skips empty, '.', '..' and separator- or drive-bearing slugs as defense in depth; discovery keeps its ensure_path_within confinement. Co-authored-by: Copilot App <223556219+Copilot@users.noreply.github.com>
APM Review Panel:
|
| Persona | B | R | N | Takeaway |
|---|---|---|---|---|
| Python Architect | 0 | 0 | 1 | Clean single-owner extension; lockfile owns the staging record and the linter guards path-shape leaks. Nit folded. |
| Supply Chain Security Expert | 0 | 1 | 1 | Path safety adequate on write and read; staged hashes were computed but discarded (deferred to #3718). Slug nit folded. |
| Test Coverage Expert | 0 | 2 | 0 | Both decisions defended at lifecycle tier; migration and warning-count gaps folded. |
B = blocking-severity findings, R = recommended, N = nits.
Counts are signal strength, not gates. The maintainer ships.
Top 1 follow-ups
- [Supply Chain Security Expert] Persist staged file hashes so on-disk edits to compile input are detected before
apm compilemerges it -- additive hardening beyond the approved [BUG] Installing a bundle for Codex, Gemini or OpenCode always failsapm audit --ciwith missing deployed files #3705 decision; tracked in Record content hashes for bundle compile staging so edits beforeapm compileare detected #3718.
Recommendation
Merge for 0.36.0 once CI is green. The deferred staged-file integrity binding is tracked in #3718; the surface it addresses existed identically before this PR and is narrowed here by the lockfile-proven-roots-only discovery rule.
Full per-persona findings
Python Architect
- [nit]
staged_file_hashescomputed inintegrate_local_bundlebut never consumed atsrc/apm_cli/install/services.py
Dead data in the return dict. Folded in bf33db0.
Supply Chain Security Expert
- [recommended] Staged file hashes are computed but never persisted, so on-disk tampering of staged compile input goes undetected at
src/apm_cli/install/local_bundle_handler.py
Deferred: tracked in Record content hashes for bundle compile staging so edits beforeapm compileare detected #3718. - [nit]
local_staging_slugs()does not reject traversal segments itself atsrc/apm_cli/deps/lockfile.py
Folded in bf33db0 withtest_staging_slugs_reject_unsafe_roots.
Test Coverage Expert
- [recommended] Pre-[BUG] Installing a bundle for Codex, Gemini or OpenCode always fails
apm audit --ciwith missing deployed files #3705 lockfile migration had no lifecycle test through the real binary attests/integration/test_local_bundle_compile_only_targets_lifecycle.py
Folded in 4fa11d4:test_bundle_reinstall_migrates_pre_3705_staging_claims(mutation-checked). - [recommended] Codex skip test did not assert the total warning count
Folded in 4fa11d4.
This panel is advisory. It does not block merge. Re-apply the
panel-review label after addressing feedback to re-run.
Generated by autopilot-pr-review-worker. This comment is AI-generated and may contain errors.
) Copilot review folds on #3717: - apm prune now plans staging records whose apm_modules/<slug> root is already gone (LockFile.absent_staging_slugs) before its early return and retires them, so a recreated directory is no longer lockfile-proven compile input. Dry runs only report; failed deletions keep their rows. - record_local_bundle_files migrates every prior bundle-owned staging claim into local_staged_files through the shared local_staging_slug classifier, not only paths re-staged this run, so an omitted or collision-skipped instruction no longer keeps apm audit --ci failing. Bytes are untouched. Co-authored-by: Copilot App <223556219+Copilot@users.noreply.github.com>
Co-authored-by: Copilot App <223556219+Copilot@users.noreply.github.com>
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Description
Follow-up to the 0.36.0 round-2 sweep. It implements the two maintainer decisions for bundle installs on compile-only targets.
no longer recordsapm_modulescompile staging as deployed files. The staging is recorded in a newlocal_staged_fileslockfile field, soapm audit --cipasses after a clean install,apm compilestill merges it, andapm prune` removes it. Older lockfiles keep compiling.[!]warning per skipped agent, instead of writing invalid.codex/agents/*.toml. Targets that deploy Markdown agents natively are unchanged.install/local_bundle_paths._UNSUPPORTED_PLUGIN_FORMAT_IDS, the same pathgemini_commanduses); guardinstall-deployment-bundle-native-layoutnow witnesses the format set.tests/unit/install/test_install_local_bundle.py::test_packed_markdown_agents_are_skipped_for_codex_with_one_warning_eachPer-target rendering of bundle agents for Codex (option 1 of #3706) is tracked separately for 0.37.
Issue and approved scope
Issue: Fixes #3705, Fixes #3706
Human scope-approval comment: maintainer decisions recorded on #3705 and #3706 (sweep record #3649 (comment)).
Fixes #3705
Fixes #3706
Type of change
Testing
APM_BINARY_PATH=.venv/bin/apm pytest -p no:xdist tests/integration/test_local_bundle_compile_only_targets_lifecycle.py tests/unit/deps/test_lockfile_local_staging.py tests/unit/install/test_install_local_bundle.py(new guards)pytest -p no:xdist tests/unit/{install,deps,primitives,compilation,commands,policy}+ prune, spec lockfile reqs, bundle e2e and pack suitesuvx ruff@0.15.12 check/format --check, pylint R0801,lint-auth-signals.sh,lint-architecture-boundaries.shSpec conformance (OpenAPM v0.1)
CONFORMANCE.{md,json}regeneratedlocal_staged_filesis an implementation-level lockfile extension (schemas allow additional properties);apm-spec-waiver:in the [BUG] Installing a bundle for Codex, Gemini or OpenCode always failsapm audit --ciwith missing deployed files #3705 commit.