[chelsealong]

Description

Fixes #5002. Updating an extension now refreshes commands and native skills for integrations recorded in its previous registry entry, including a non-default Codex integration. An integration with no prior registration remains untouched.

Testing

• Regression test: failed before the fix because the Codex SKILL.md was deleted; both positive and negative cases pass after the fix.
• .venv/bin/python -m pytest tests/specify_cli/extensions/test_command_update.py tests/specify_cli/extensions/test_command_update_transaction.py tests/specify_cli/extensions/test_command_update_artifacts.py -q — 61 passed.
• .venv/bin/specify --help and git diff --check — passed.
• Ruff reports 20 findings in the touched files; the unchanged files report the same 20 findings.

AI Disclosure

• I used AI assistance.

AI disclosure: Codex (GPT-6, autonomous mode) investigated the issue and generated the code and regression test. No human review is claimed.

[Copilot]

🟡 Changes recommended

Secondary registration can overwrite the active integration’s skills when output directories are shared.

2 open issues

• Preserve safeguards when refreshing prior integrations · New
• Add rollback coverage for failed post-install registry refresh · New

What changed in this PR

Preserves extension commands and native skills for previously registered integrations during updates, addressing #5002.

Changes:

• Refreshes previously registered non-default integrations.
• Includes their outputs in transactional backups.
• Adds positive and negative Codex regression cases.

AI disclosure: GitHub Copilot (model unknown, autonomous) generated this review for the requester.

File	Description
tests/​specify_cli/​extensions/​test_command_update.py	Tests preservation of registered Codex skills and exclusion of unregistered integrations.
src/​specify_cli/​extensions/​_command_update_transaction.py	Expands backups and restores secondary integration registrations after installation.

_{Review effort: Max}

[mnriem]

Please address Copilot feedback

[chelsealong]

Thank you for both findings. Commit 3542570 reuses the refreshed command list when integrations share a skills directory, preserving the active integration’s rendering. Secondary integrations now retain the normal output-directory and project-marker checks.

The new CLI regressions cover shared Codex/Zed output, a deleted output directory, a removed Hermes project marker, and failure after secondary registration has overwritten an existing candidate and created new alias files. The rollback test checks byte-for-byte restoration, removal of the new directories, and equality with the original registry entry. Removing the expanded backup inventory makes that test fail with leftover files. The three affected suites pass all 93 tests, and the CLI help entry point succeeds.

Posted on behalf of chelsealong. Codex (model GPT-6, autonomous) implemented the follow-up, ran the tests, and drafted this summary.

[Copilot]

🟡 Changes recommended

Secondary-integration updates can overwrite existing user files and delete their only backups during cleanup, creating a data-loss risk.

8 open issues

• Protect unowned command and prompt files from overwrite · New
• Skip fallback commands when replacement skills are rendered · New
• Include active skills roots in the overwrite guard · New
• Fail and roll back incomplete secondary registration · New
• Document refresh behavior for inactive registered integrations · New
• Reuse registrar policies in the refresh pass · New
• Move rollback coverage into the transaction test module · New
• Add rollback coverage for failed post-install registry refresh

3 previously missed issues

In code that hasn't changed since last review

Apply refresh eligibility checks to historical backup targets

src/​specify_cli/​extensions/​_command_update_transaction.py:419

Historical targets bypass the output-directory and detect_dir checks used by the refresh pass, so a removed Hermes marker can make an unrelated hard-linked skill at a new alias abort the entire update. Apply those checks before adding secondary backup targets, while preserving the manager's active recovery targets and the backups of previously registered files.

AI-generated for the review requester by GitHub Copilot (model unknown, autonomous mode).

Preserve previously registered Copilot skills during integration changes

src/​specify_cli/​extensions/​_command_update_transaction.py:570

An extension previously used by Copilot in --skills mode is tracked only in registered_skills, so updating after integration use claude still deletes its Copilot skills. Capture the previously owned skill roots before removal and refresh those integrations in their original skills mode.

AI-generated for the review requester by GitHub Copilot (model unknown, autonomous mode).

Refresh persisted generic registrations when inactive

src/​specify_cli/​extensions/​_command_update_transaction.py:580

After integration use claude, the registrar omits generic from AGENT_CONFIGS, so this filter drops a prior generic registration even though removal has deleted its hash-owned command files. Resolve the persisted generic directory and refresh its commands and ownership hashes even when generic is inactive.

AI-generated for the review requester by GitHub Copilot (model unknown, autonomous mode).

1 resolved since last review

• Preserve safeguards when refreshing prior integrations

_{Review effort: Max}