[kitlangton]

An unrelated config edit currently rebuilds the entire configured skill catalog. For example, changing only shell triggers another directory scan, remote skill index pull, watcher teardown/recreation, and skill reload even though the source list is unchanged.

Compare the derived, deduplicated skill-source descriptors in order before refreshing on config.updated, while still retaining the latest config entries. This preserves path expansion and later-source precedence. Source additions, removals, reordering, and URL changes still refresh; filesystem events still refresh unconditionally, including symlink retargeting and missing-directory creation. Unrelated config edits consequently no longer act as incidental remote skill index refreshes.

Regression coverage counts actual filesystem scans (delegating to FSUtil), discovery calls, catalog reloads, and watcher subscriptions. Before the fix, the unrelated shell edit increased scans/pulls/reloads by one each; afterward all three remain unchanged. It also checks equivalent relative/absolute paths, duplicates, source ordering, replacement/removal, and skill edits after a source change.

Validation:

• 25 skill/config-skill/discovery/plugin-skill tests pass.
• Broader config suite: 155 pass, one file-recreation watcher timeout; that test passes in isolation and only constructs Config/Bus, not the skill plugin.
• bun typecheck in packages/core passes; focused oxlint and git diff --check pass.
• Local fixture suites needed execution outside the filesystem/network sandbox and ran with Bun 1.4.0. Subsequently ran the normal .husky/pre-push hook with temporary Bun 1.4.1 (no global installation change): version check passed and all 33 typecheck tasks succeeded (25 cache hits, 8 executed), exit code 0. Turbo emitted sandbox IO warnings but no task failed. This closes the validation gate initially bypassed during push.

This PR is independent of the skill plugin startup read/subscribe gap fix.

[github-actions]

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