Doesn't clean submodules before creating branch

[daquinteroflex]

Currently, when the action is checked out, it checks out from the base directory which may include sub modules that are not in the new_branch_ref branch and it does not clean that history. This creates issues onwards.

[GuillaumeFalourd]

Thank you for opening the issue @daquinteroflex 🚀

I may not be able to correct this right away though 😨

I observed in you commentary on the flexcompute/tidy3d repository that you could eventually "sit down and fix the action for our intentions". I don't know how urgent it is, but feel free to contribute to the action (even if not for this issue). The more contributors, the better! 😄