fix(extensions): rewrite extension-relative paths in generated SKILL.md files

[mbachorik]

Fixes #2101

What

When an extension command body references files relative to the extension
root (e.g. agents/control/commander.md, knowledge-base/scores.yaml),
those paths are now correctly rewritten to .specify/extensions/<id>/...
in the generated SKILL.md files.

Why

Extension commands are registered as SKILL.md files for skill-format agents
(currently kimi and codex). After installation the extension files live
at .specify/extensions/<id>/..., but render_skill_command() had no path
rewriting — it wrote bare relative paths verbatim. The AI agent resolves
them from the workspace root where they don't exist, so the referenced files
were never found.

How

• Add CommandRegistrar.rewrite_extension_paths(text, extension_id, extension_dir): discovers which subdirectories exist in the installed extension and rewrites matching subdir/… references to .specify/extensions/<id>/subdir/… using conservative regex boundary anchoring
• Run it before resolve_skill_placeholders() so extension-local scripts/ and templates/ aren't incorrectly redirected to project-level paths
• Thread source_dir from register_commands() through to render_skill_command() for both primary commands and aliases

Tests

Unit tests in test_extensions.py:

• Core fix: codex, all subdir types (agents/, templates/, scripts/, knowledge-base/)
• Kimi agent receives the same rewriting
• Alias commands are also rewritten
• Extension with no subdirs — text unchanged (conservative)

Integration tests in test_integration_extension_skill_paths.py:

• Skipped unless SPECKIT_TEST_EXT_DIR env var points to a local extension checkout
• Installs real extension, verifies all skill files end-to-end

🤖 Generated with Claude Code

[Copilot]

Pull request overview

This PR fixes extension command bodies that reference extension-root-relative files (e.g., agents/..., knowledge-base/...) by rewriting those references to the installed location under .specify/extensions/<id>/... when generating SKILL.md files for skill-format agents (notably codex and kimi).

Changes:

• Add CommandRegistrar.rewrite_extension_paths() and invoke it during SKILL.md rendering (before placeholder resolution).
• Thread source_dir through SKILL.md generation for primary commands and aliases so the renderer has enough context to rewrite paths.
• Add unit tests (extensions) and an opt-in integration test (real extension install) to validate end-to-end behavior.

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 1 comment.

File	Description
src/specify_cli/agents.py	Adds extension-relative path rewriting and applies it during SKILL.md rendering; threads source_dir into SKILL.md generation paths.
tests/test_extensions.py	Adds unit tests covering extension path rewriting for codex/kimi, aliases, and conservative “no subdirs” behavior.
tests/test_integration_extension_skill_paths.py	Adds opt-in integration tests that install a real extension and validate rewritten paths across generated skill files.

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[Copilot]

render_skill_command() rewrites paths whenever source_dir is provided, but register_commands() always passes source_dir for all sources (extensions and presets). For presets, source_dir typically contains a templates/ directory, so this logic will rewrite any templates/... references in preset command bodies to .specify/extensions/<preset-id>/templates/..., which is an incorrect location and can break preset-generated SKILL.md files.

Consider gating this rewrite so it only runs for extensions (e.g., only when an extension.yml is present in source_dir, or by threading an explicit is_extension/installed_prefix into render_skill_command()), rather than applying it to every SKILL.md source directory.