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.