Correctly handle module files missing from a previously patched save

[Danielv123]

Resolves #611

Logs missing files instead of throwing an error.

[Cooldude2606]

Log a warning that the file went missing. The current patch logic already replaces all patched in files with files from the modules to patch in.

The above is implemented as was suggested by Hornwitser.
However, is leaving the empty buffers in the map a good idea?

As seen by your edit to line 398/405 you needed to add a check to account for non-existent files in the map.
In the future if we provided a method to extract and save modules from a save file, then we would end up writing empty files if we didnt also account for the empty buffers.
In your issue this was a git ignore file that went missing, and I'd argue an incorrectly empty one is more dangerous than no file at all.

This can be fixed with a .filter after the .map, should we?