Project Files checkbox can be inaccurate when collapsing and expanding directories

If the Files API takes awhile due to a very large directory size, and the user clicks a checkbox to include/exclude a item; the checkbox could be inaccurate when the parent directory is then collapsed and re-expanded.

This is due to the item being removed then re-added to the DOM upon collapsing and expanding. We do not store a local state of included/excluded files and instead rely on the API response. This reliance also explains why including/excluding a directory does not change nested files until we hear back from the Files API.

Ideally the expanded state of a directory shouldn't affect the checkbox state prior to the hearing back from the Files API.

This issue does not include handling nested files when a directory is included in the deployment.

Start by tracing the Files API-backed Project Files checkbox and the directory collapse/expand path. Reproduce the delayed-response case with a large directory, then verify that collapsing and re-expanding preserves the user's include/exclude choice before the API responds. Keep nested-file handling out of scope, as stated in the issue.