fix extension-local script path rewriting

[ZhiyaoWen999]

Summary

Fixes #3358.

Extension command materialization now keeps extension-owned scripts/... references under .specify/extensions/<extension_id>/scripts/... instead of rewriting them to core .specify/scripts/....

Root Cause

CommandRegistrar.rewrite_project_relative_paths() treated every top-level scripts/ reference as a core project script. That is correct for built-in commands and ../../scripts/... references, but extension command sources may use scripts/... to refer to helper scripts shipped inside the extension archive.

During skills/materialization, those paths were rewritten to .specify/scripts/..., where extension helper scripts do not exist.

Changes

• Added optional extension context to script path rewriting and skill placeholder resolution.
• Passed the installed extension id through extension command and skill registration paths.
• Preserved existing behavior for core scripts such as ../../scripts/..., which still resolve to .specify/scripts/....
• Added regression coverage for direct path rewriting and auto-registered extension skills.

Validation

• PYTHONPATH=src .venv/bin/python -m ruff check src/specify_cli/agents.py src/specify_cli/extensions/__init__.py tests/test_extensions.py tests/test_extension_skills.py
• PYTHONPATH=src .venv/bin/python -m pytest tests/test_extensions.py tests/test_extension_skills.py -q
• PYTHONPATH=src .venv/bin/python -m pytest tests/test_presets.py -q
• git diff --check

AI Disclosure

I used Codex to investigate the issue, implement the fix, add tests, and run validation. I reviewed the code paths and test results before submitting.

[Copilot]

Pull request overview

This PR fixes extension command materialization so that extension-owned scripts/... references remain extension-local under .specify/extensions/<extension_id>/scripts/... instead of being rewritten into core .specify/scripts/..., addressing #3358.

Changes:

• Added an optional extension_id context to CommandRegistrar.rewrite_project_relative_paths() and plumbed it through command/skill rendering flows.
• Updated extension command + skill registration to pass manifest.id so top-level scripts/ resolves into the installed extension directory when materializing extension content.
• Added regression tests covering both direct path rewriting and auto-registered extension skills.

Show a summary per file

File	Description
src/specify_cli/agents.py	Adds extension_id-aware rewriting so extension scripts/ paths resolve under .specify/extensions/<id>/scripts/ during rendering.
src/specify_cli/extensions/__init__.py	Passes manifest.id through extension registration/materialization so extension context is applied consistently.
tests/test_extensions.py	Extends unit coverage for _adjust_script_paths() and rewrite_project_relative_paths() with extension context behavior.
tests/test_extension_skills.py	Adds regression coverage ensuring auto-registered skills preserve extension-local script paths and don’t rewrite into .specify/scripts/.

Review details

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• Files reviewed: 4/4 changed files
• Comments generated: 0
• Review effort level: Low