[Refactor] Improve copyDirectoryContents efficiency and cleanup knip config

[gonzaloriestra]

WHY are these changes introduced?

The current implementation of copyDirectoryContents was inefficiently performing manual string replacements on absolute paths to calculate relative destination paths. Additionally, the knip configuration contained stale ignoreDependencies entries.

WHAT is this pull request doing?

1. Refactored copyDirectoryContents: Used the cwd option in glob to directly obtain relative paths, eliminating the need for brittle manual path stripping. Simplified the copy loop using Promise.all with map.
2. Cleaned up knip configuration: Removed unused @graphql-typed-document-node/core entries from ignoreDependencies in package.json for both packages/app and packages/cli-kit.
3. Documented Learnings: Added key performance and refactoring insights to .jules/refactor.md and .jules/bolt.md.

How to test your changes?

Run the unit tests for cli-kit's filesystem utilities:

pnpm --filter @shopify/cli-kit vitest run src/public/node/fs.test.ts

Verify that knip no longer reports configuration hints:

pnpm knip

Checklist

• I've considered possible cross-platform impacts (Mac, Linux, Windows)
• I've considered possible documentation changes
• I've considered analytics changes to measure impact
• The change is user-facing — I've identified the correct [bump type] and added a changeset with pnpm changeset add

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PR created automatically by Jules for task 1894134398803177433 started by @gonzaloriestra

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