fix: resolve __SPECKIT_COMMAND_*__ refs in preset skill rendering (#2717)

[huy1010]

Description

Presets that override core commands under the agent skill layer (e.g. Claude with --ai-skills) were leaking raw __SPECKIT_COMMAND_*__ placeholders into the generated SKILL.md instead of rendering them as slash-command invocations like /speckit-plan.

Root cause: the preset skill-rendering paths in src/specify_cli/presets.py ran only resolve_skill_placeholders(), whereas the command layer (CommandRegistrar.register_commands()) additionally calls IntegrationBase.resolve_command_refs(). The skill paths never resolved the command-reference tokens — {ARGS} → $ARGUMENTS resolved correctly, so only the command tokens leaked, matching the report.

Fixes #2717. This is a concrete instance of the path divergence tracked in #1976.

Change: added a small shared helper PresetManager._resolve_skill_command_refs() that maps the agent's invoke separator to resolve_command_refs(), and called it right after resolve_skill_placeholders() in every preset skill-rendering path:

• _register_skills() — preset install (the path reported in the issue)
• _reconcile_skills() — override-restoration block
• _unregister_skills() — both restore paths (core + extension templates)

The issue's proposed patch covered only _register_skills(); I extended the same one-line fix to the sibling restore/reconcile paths because they share the identical omission and would otherwise still leak tokens on preset removal / reconciliation. extensions.py is intentionally left out of scope (separate concern).

Testing

• Tested locally with uv run specify --help
• Ran existing tests with uv sync && uv run pytest — 2988 passed, 35 skipped
• Tested with a sample project (Claude --ai-skills: preset add --dev + preset remove)

⚠️ Note for reviewers: uv run specify served a stale cached wheel (project version 0.8.15.dev0 unchanged → uv build-cache hit), so it kept showing the pre-fix behavior even after uv pip install -e .. I verified working-tree behavior by invoking .venv/bin/specify directly. Worth flagging since the documented uv run specify flow can silently exercise old code when the dev version string is unchanged.

Manual test results

Agent: Claude Code (CLI) | OS/Shell: macOS / zsh

Repro: scaffold a Claude --ai-skills project, install a local preset overriding speckit.specify whose body references __SPECKIT_COMMAND_PLAN__ / __SPECKIT_COMMAND_TASKS__, then remove it (restoring from a core template that also carries the tokens). Inspected .claude/skills/speckit-specify/SKILL.md.

Command tested	Notes
specify init --integration claude	Skills installed to .claude/skills; speckit-specify present
specify preset add --dev <preset>	SKILL.md renders /speckit-plan, /speckit-tasks; 0 raw __SPECKIT_COMMAND_*__ (was 2 before the fix)
specify preset remove <preset>	Restored SKILL.md renders /speckit-plan; 0 raw tokens (was 1 before the fix)

Test selection reasoning

Changed file	Affects	Test	Why
src/specify_cli/presets.py	specify preset add / remove, preset skill overrides	T1–T3	Rule: src/specify_cli/*.py → CLI preset commands; preset command overrides mirror into the skill layer

Required tests (prerequisites first):

• T1: specify init --integration claude — scaffold the skills layer (prerequisite for T2/T3)
• T2: specify preset add --dev — install path (_register_skills)
• T3: specify preset remove — restore path (_unregister_skills); requires T2

New automated regression tests added in tests/test_presets.py: test_register_skills_resolves_command_refs (install) and test_restore_skill_resolves_command_refs (restore). Both fail on main and pass with the fix.

AI Disclosure

• I did use AI assistance (describe below)

This PR was developed with Claude Code (Anthropic): issue analysis, the patch, and the regression tests were AI-generated. The full pytest suite and the manual CLI install/remove cycle reported above were run as part of development, and the change was reviewed (including a follow-up pass to remove a lint-suppression # noqa in favor of a top-level import and to make the helper docstring describe behavior) before submission.