fix(codex): native skills fallback refresh + legacy prompt suppression

[RbBtSn0w]

Background

This is a follow-up fix after the previous skills/frontmatter work was already merged.

In local debugging and re-init scenarios (specify init --here --ai codex --ai-skills), two issues were observed:

1. Older release assets can still contain legacy Codex prompt layout (.codex/prompts), which should not appear in skills mode.
2. For native-skills agents (Codex/Kimi), when bundled skills are not usable and fallback conversion is required, existing SKILL.md files were not refreshed due to additive-only behavior.

Why this change

The goal is to make Codex/Kimi skills-mode initialization resilient without broad behavioral changes:

• Keep current default behavior for non-native flows.
• Only adjust the native fallback path where stale/missing bundled skills cause functional issues.

What changed

1. Skip legacy Codex prompt directory in skills mode

• In download_and_extract_template(...), add skip_legacy_codex_prompts.
• When ai=codex and --ai-skills is enabled, do not materialize .codex from the downloaded archive.

2. Native fallback compatibility

• For native-skills agents, if bundled skills are not detected, call install_ai_skills(...) as fallback instead of failing immediately.
• Keep explicit failure if both bundled skills and fallback conversion are unavailable.

3. Minimal-impact overwrite policy

• Add overwrite_existing: bool = False to install_ai_skills(...).
• Preserve default additive behavior globally.
• Enable overwrite only in native fallback branch (overwrite_existing=True) so fallback can refresh stale native SKILL.md files.

Why this is minimal impact

• No global overwrite behavior change.
• No behavior change for non-native agents.
• Existing additive semantics remain the default API contract.
• Scope is limited to Codex/Kimi fallback path and legacy Codex prompt suppression in skills mode.

Tests

• Updated native-fallback tests to assert fallback invocation and overwrite flag usage.
• Added coverage for overwrite-enabled replacement of existing SKILL.md.

Validation run:

• uv run pytest tests/test_ai_skills.py -q -> 89 passed

[Copilot]

Pull request overview

This PR tightens Codex skills-mode initialization by avoiding legacy .codex prompt extraction and making native-skills agents (Codex/Kimi) attempt an install_ai_skills() fallback when bundled skills are missing, with updated tests and documentation to reflect the skills-based Codex layout.

Changes:

• Add skip_legacy_codex_prompts support to template extraction and enable it for codex + --ai-skills.
• For native-skills agents, attempt install_ai_skills() fallback when bundled skills are missing; keep a clear error when both bundled skills and fallback fail.
• Update tests, docs, and release-package skill generators to align SKILL.md frontmatter.

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
src/specify_cli/__init__.py	Adds legacy .codex skip/removal during extraction and implements native-skills fallback behavior in init.
tests/test_ai_skills.py	Updates Codex native-skills tests to assert fallback is attempted and non-speckit skill dirs trigger fallback.
src/specify_cli/agents.py	Adds a technical-debt note documenting expected SKILL.md frontmatter schema alignment.
AGENTS.md	Updates Codex directory documentation to .agents/skills/ and adjusts directory conventions section.
.github/workflows/scripts/create-release-packages.sh	Adds compatibility and metadata fields to generated SKILL.md frontmatter.
.github/workflows/scripts/create-release-packages.ps1	Mirrors the SKILL.md frontmatter additions for PowerShell packaging.

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