fix: write Codex dev skills as files

[sjh9714]

Description

Fixes #2930.

specify extension add --dev created symlinked Codex SKILL.md files, but Codex currently does not load those symlinked skills. This keeps dev-mode symlinks for other agents while writing Codex SKILL.md outputs as regular files in both the agent command registration path and the extension skill registration path.

Normal non-dev installs are unchanged, and existing Copilot dev symlink behavior remains covered by the existing test.

Testing

• Tested locally with uv run specify --help
• Ran existing tests with uv sync && uv run pytest
• Tested with a sample project (if applicable)

Commands run:

• uv run --extra test pytest tests/test_extensions.py -k "add_dev_writes_codex_skills_as_files" -q (failed before the fix, passed after)
• uv run --extra test pytest tests/test_extensions.py -q
• uv sync --extra test && uv run pytest -q
• uv run specify --help
• git diff --check

AI Disclosure

• I did not use AI assistance for this contribution
• I did use AI assistance (describe below)

Codex assisted with issue scouting, code-path inspection, and local review. I reviewed the final diff and ran the listed checks locally.

[mnriem]

Thanks for tracking this down — the bug in #2930 is real and the behavior here is correct: Codex can't load symlinked SKILL.md files, so writing them as real files is the right outcome.

My concern is with how it's special-cased rather than the fix itself. The change hardcodes agent_name == "codex" in CommandRegistrar._write_registered_output (agents.py) and selected_ai != "codex" in _register_extension_skills (extensions.py). Both are generic, agent-agnostic code paths, and we have an integration architecture specifically so per-agent knowledge lives in one declarative place. AGENT_CONFIGS is already derived from INTEGRATION_REGISTRY via _build_agent_configs(), and CodexIntegration is a clean self-contained class — "Codex can't use dev symlinks" really belongs there, not in shared plumbing. (The existing agent_name == "copilot" carve-out is the same debt; I'd rather not grow it.)

Could we route this through integration metadata instead? Roughly:

1. Add dev_no_symlink = True to CodexIntegration and propagate it into the config dict in _build_agent_configs() the same way invoke_separator already is.
2. In _write_registered_output, swap the string check for a metadata lookup:

   if not link_outputs or agent_config.get("dev_no_symlink"):

3. In _register_extension_skills, replace selected_ai != "codex" with link_outputs and not agent_config.get("dev_no_symlink").

This follows the existing inject_name convention (opt-in flag, absent means the established default of symlinking), keeps the constraint owned by the Codex integration as the single source of truth, and means any future agent with the same limitation just sets the flag — no edits to shared code. The test you added is great and would carry over almost unchanged.

[Copilot]

Pull request overview

This PR addresses issue #2930 by ensuring that Codex dev-mode extension installs write SKILL.md artifacts as real files (not symlinks), because Codex does not load symlinked skills. It adds a dev_no_symlink integration flag and threads it through command/skill registration to selectively disable symlink outputs for Codex while preserving existing dev symlink behavior for other agents.

Changes:

• Add dev_no_symlink integration metadata (default False, enabled for Codex) and propagate it into agent registrar configs.
• Update dev-mode output writing for agent commands and extension skills to honor the no-symlink policy.
• Add regression tests validating Codex dev installs write non-symlink SKILL.md outputs and that the policy is exposed in config.

Show a summary per file

File	Description
tests/test_extensions.py	Adds a regression test ensuring Codex dev installs create SKILL.md as a regular file.
tests/test_agent_config_consistency.py	Verifies Codex exposes dev_no_symlink in CommandRegistrar.AGENT_CONFIGS.
src/specify_cli/integrations/codex/init.py	Declares dev_no_symlink = True for Codex integration.
src/specify_cli/integrations/base.py	Introduces the dev_no_symlink integration attribute.
src/specify_cli/extensions.py	Adjusts extension skill registration to avoid dev symlinks when dev_no_symlink is set.
src/specify_cli/agents.py	Threads agent_config into output writer and disables dev symlinks when dev_no_symlink is set.

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• Files reviewed: 6/6 changed files
• Comments generated: 2