Symlink embedded packages instead of copying

[hacha]

Summary

• Embedded package folders directly under Packages/ are now symlinked instead of copied when cloning a project
• Root-level files (manifest.json, packages-lock.json, etc.) are still copied as before
• Integrity validation updated to only check root-level files (symlinked folders don't need syncing)

Motivation

When developing local/embedded packages directly under Packages/, the current behavior of copying the entire directory means changes in the clone are not reflected in the original project and vice versa. By symlinking the subdirectories, embedded packages are shared between the original and clone, which is essential for library development workflows.

Test plan

• Create a clone of a project that has embedded packages under Packages/
• Verify that manifest.json and packages-lock.json are copied (not symlinked)
• Verify that package subdirectories under Packages/ are symlinked
• Edit a file in an embedded package from the clone and confirm the change appears in the original
• Reopen the clone and verify that root-level file validation still works correctly