feat: add ability to customize `paths` in `skills.sh.json`

• minorFast path can silently drop declared skills if the config fetch failssrc/blob.tsL480–491Also in Review
• nitPath containment is lexical; symlinked folders are not resolvedsrc/skills-sh-config.tsL34–41

  This is the same gap the existing skills/ folder and the plugin-manifest isContainedIn check already have, so it is not a new exposure.

2 major2 minor

• majorFailed skills.sh.json download silently drops declared skillssrc/blob.tsL489–490

  fetchSkillsShPaths checks that skills.sh.json is in the tree, then maps a failed raw download (timeout or HTTP error) to []. That is the same result as having no config. findSkillMdPaths still finds the standard skills, so tryBlobInstall succeeds and the caller never falls back to git clone. The install reports success but leaves out every skill in the declared folders. All three reviewers raised this.

  Fix

  When the tree has skills.sh.json but fetchRawContent returns null, return null from tryBlobInstall so the caller uses clone discovery. Keep treating config that downloads but does not parse as an empty paths list. Add a test where the config download fails next to an installable standard skill.

• majorGitHub fast path keeps duplicate skill namessrc/blob.tsL648–670

  The docs and the new disk test say only the first skill with a given name is kept. tryBlobInstall adds every parsed SKILL.md to parsedSkills without checking names. A declared folder whose skill shares a name with one under skills/ yields two BlobSkills. Both are installed into the same folder. getSkillRepoPaths (src/add.ts:1356-1359) then records the later, declared path in the lock, so updates track the lower-priority copy. All three reviewers raised this.

  Fix

  In tryBlobInstall, drop later parsedSkills entries whose name was already seen, before downloading snapshots, so the first match and its repoPath are kept. Add a blob test that mirrors the existing disk test for standard versus declared duplicate names.

• minorDocs say repository root, but the config is read from the subpathdocs/creating-skills.mdL142

  Both discoverSkills (searchPath = basePath + subpath) and fetchSkillsShPaths read skills.sh.json from the folder being searched, and resolve ./ entries from there. The plugin manifest lookup works the same way. When a subpath is given, a root skills.sh.json is ignored. No test covers a subpath.

  Fix

  Change the docs to say skills.sh.json is read from the folder being searched (the repository root, or the subpath when one is given), with entries relative to that folder. Consider adding one subpath test for each discovery path.

• minorAGENTS.md architecture list misses the new filesAGENTS.mdL42

  AGENTS.md lists plugin-manifest.ts and its test, but not src/skills-sh-config.ts or tests/skills-sh-paths.test.ts.

  Fix

  Consider adding both files to the architecture list.

• minorDuplicate-name docs claim doesn't hold on GitHub blob pathdocs/creating-skills.mdL151

  Blob path listed 'alpha' twice when skills/ and a declared path both define it; disk walk keeps first. Pre-existing for skills/ duplicates, but paths makes it easier to hit.

• nitSymlinked declared path is followed outside the reposrc/skills-sh-config.tsAlso in Security

2 minor1 nit

• minorPublished CLI documents a new paths fielddocs/creating-skills.mdL140–151

  Once released, repo authors may move skills under declared folders. After a revert, add/use/update stop finding them there (files untouched). Users pinned to the release keep the feature until they upgrade.

• minorLock entries pointing into declared folderssrc/update.tsL720

  Skills installed from a declared folder keep a skillPath there. After a revert, update checks still work via the saved path, but reinstalls re-run discovery (update.ts:720, :991), which won't find them. Those updates fail until reinstalled by hand; nothing is corrupted.

• nitExtra fetch only when skills.sh.json existssrc/blob.tsL476–491

  Raw fetch happens only if the repo tree lists the file; nothing cached or stored.

3 minor

• minorSymlinked declared folder can reach outside the reposrc/skills-sh-config.tsL39–45

  Paths are checked as text only. A repo with tools/skills -> /some/local/dir and paths ['./tools/skills'] makes discovery read that directory (reproduced). Not new: a symlink named skills/ already does the same without any config.

  Fix

  Resolve each search folder with realpath and require it to stay under realpath(searchPath).

• minorUnbounded paths list with quadratic de-duplicationsrc/skills-sh-config.tsL44

  There's no cap on entries, and result.includes makes de-duplication O(n^2). 50,000 entries (539 KB) took about 3 s to parse; a few MB would stall add/update for minutes.

  Fix

  De-duplicate with a Set and ignore entries after the first ~100.

• minorBlob path silently drops declared folders when the config fetch failssrc/blob.tsL480–490Also in Review