fix: preserve generated skill links

[creatornader]

Summary

• Preserve generated skill paths when the frontmatter name differs from the source directory.
• Verify each generated index link points to an existing generated skill file.

Tests

• bun test test/llms-txt-shape.test.ts

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[creatornader]

This PR is the generated-link repair split out from #2083 in response to review. It keeps the generator tied to each skill's generated output path and verifies every indexed link exists. #2083 will rebase onto main after this lands, so its command rename no longer carries this unrelated repair.

[creatornader]

/trunk merge

[trunk-io]

An error occurred while submitting your PR to the queue: Only users that are a part of this repo's Trunk organization or have write permissions to the repo can submit a PR to the queue

[creatornader]

Trunk rejected my submission because this fork account does not have write access to the repository. This isolated link repair is ready for a maintainer to submit. Once it lands, I will immediately rebase #2083 onto main and remove the duplicated repair from that PR.