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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[mbachorik]

Fixed the path-rewriting scope issue raised in the inline review.

Change: Gated rewrite_extension_paths() in render_skill_command() on (source_dir / "extension.yml").exists(). This ensures the rewrite only applies to extension source directories; preset directories (which have preset.yml but no extension.yml) are skipped entirely.

Test added: test_preset_skill_registration_does_not_rewrite_paths — sets up a preset-style dir with a templates/ subdir, registers commands, and asserts the output contains no .specify/extensions/... paths.

[Copilot]

Pull request overview

This PR fixes extension command SKILL.md generation so that references to extension-relative files (e.g., agents/..., templates/...) are rewritten to their installed location under .specify/extensions/<id>/..., making those files resolvable by skill-format agents (Codex/Kimi). It addresses issue #2101 where generated SKILL.md files contained bare relative paths that don’t exist from the workspace root.

Changes:

• Add extension-relative path rewriting during SKILL.md rendering and thread source_dir through skill rendering for primary commands and aliases.
• Add unit tests covering rewriting across multiple subdirs, Kimi support, aliases, and “no subdirs” conservative behavior.
• Add an opt-in integration test (env-var gated) that installs a real extension and validates end-to-end SKILL.md outputs.

Show a summary per file

File	Description
src/specify_cli/agents.py	Implements extension-relative path rewriting and applies it during SKILL.md rendering (with source_dir plumbing).
tests/test_extensions.py	Adds unit tests ensuring SKILL.md content rewrites extension-relative paths for Codex/Kimi and aliases.
tests/test_integration_extension_skill_paths.py	Adds env-gated integration tests to verify rewriting against a real installed extension.

Copilot's findings

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• Files reviewed: 3/3 changed files
• Comments generated: 0 new