[chelsealong]

Description

Fixes #5321. Forced init now saves the selected integration mode before re-registering installed extensions and presets, so extension files use the selected mode.

Testing

• Regression test: skills mode failed before the fix; skills and command modes pass after it.
• .venv/bin/python -m pytest tests/integrations/test_cli.py tests/test_agent_config_consistency.py -q — 111 passed.
• .venv/bin/specify --help and git diff --check — passed.
• Ruff reported 39 findings on both the unmodified baseline and the patch.

AI Disclosure

Codex (GPT-6, autonomous mode) generated the code and tests and ran local validation. No human review or testing is claimed.

[Copilot]

🟡 Changes recommended

Forced initialization can overwrite files outside the project through symlinked skill subdirectories because individual destination directories are not validated.

1 open issue

• Prevent skill writes from following symlinked subdirectories · New

What changed in this PR

Fixes #5321 by saving the selected integration mode before forced init re-registers installed extensions and presets.

Changes:

• Moves init-option persistence ahead of re-registration so it uses the current mode.
• Adds regression coverage for skills and command modes when saved options are absent.

File	Description
tests/​integrations/​test_cli.py	Verifies forced init generates extension files only in the selected mode.
src/​specify_cli/​command_init.py	Saves init options before extension and preset re-registration.

_{Review effort: Balanced (auto)}

[mnriem]

Please address Copilot feedback

[chelsealong]

Thank you for identifying the destination-directory gap. Commit 6e3f8a9 validates each skill directory with the existing safe-directory helper before any directory creation or file write.

The regression reproduces an external SKILL.md overwrite on the previous head, including through specify init --here --force. With the fix, the external bytes and directory symlink remain unchanged, while ordinary extension skills still register. The extension-skills and CLI integration suites pass all 210 tests.

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

[Copilot]

🟡 Changes recommended

Symlink setup in the extension-skills and CLI tests lacks an OSError skip guard, causing failures on Windows accounts without symlink privileges before registration is exercised.

2 open issues

• Prevent skill writes from following symlinked subdirectories
• Skip symlink tests when Windows privileges are unavailable · New

_{Review effort: Balanced (dynamic)}

[chelsealong]

I added OSError skip guards to the directory-symlink setup in both regression tests. When symlink creation succeeds, the existing assertions still run. Both affected suites pass: 210 tests. Ruff reports 35 findings on both HEAD and the patch; git diff --check and specify --help pass.

Posted on behalf of chelsealong. Codex (GPT-6, autonomous mode) made the test changes, ran validation, and drafted this reply.

Commit: 1fe9169

[Copilot]

🔵 Needs a closer look

Reordering active-mode persistence and forced initialization introduces interacting lifecycle, file-ownership, and partial-failure effects that require broader review than a straightforward local change.

1 open issue

• Prevent skill writes from following symlinked subdirectories

1 resolved since last review

• Skip symlink tests when Windows privileges are unavailable

_{Review effort: Balanced (dynamic)}