chore: speed up engine builds with incremental namespacing

[doorgan]

Drastically improves Engine load times by incrementally namespacing engine files

Rather than complicating the transformer modules to make them aware of which files should be touched and which shouldn't, we:

1. Figure out which files are new, change and which should be deleted from the output directory
2. Delete the files that are flagged for deletion in the output folder
3. Copy the new+changed files to a temporary folder
4. Namespace that folder
5. Copy the contents of the temp folder to the output folder

This achieves the same with the slight overhead of creating and cleaning up a temporary folder.

In my test on my m2 macbook I got the times down from ~10 seconds to 800-1200ms.