[cli] Fix issues with StyleX usage within external packages

At it's core, the CLI transforms an entire folder to to transform the JS and extract the CSS. This works well.

You can also manually declare external package dependencies that should be pre-compiled. However, this process is somewhat buggy today.

The task is to fix the problems with pre-compiling external packages.

## Details of the task

The CLI lets you define specific packages that should be compiled with StyleX. It is important these packages are not pre-compiled and should only have source files and not compiled files.

The CLI pre-compiles the configured packages into the output folder.

- [ ] Investigate the limitations of the current approach
- [ ] Investigate why the packages are sometimes not compiled correctly on edits. This is specially relevant to monorepos.
- [ ] Fix the bugs to ensure that the CLI reliably compiles configured packages.
- [ ] Ensure that changes in mono-repo packages are tracked and the files re-compiled on edits