feat(cli): skip missing sync files

[heimanba]

Summary

• Add agents sync --skip-missing-files for non-interactive sync runs.
• Keep the existing interactive file association prompt as the default behavior.
• Document the new option and cover the missing-file filtering logic with a unit test.

Validation

• bun test packages/cli/tests/unit/sync-file.test.ts
• bun run --cwd packages/cli typecheck
• bun test scripts/open-source.test.ts