2 directories same spelling one directory is camel cased

Howdy git gurus,

I have the dubious distinction of working with a remote repo (master) 
that has a class loader run-time error when cloned, built and executed.

The reason for the runtime issue is a directory hierarchical path has to 
directories (folders) with the same name spelling but one of the 
directories is camel-cased. The package names are the same.

The compiler doesn't care but the run-time class loader has an issue 
with the 2 'same like named' classes.

How to remove the offending directories and files at the locally cloned 
repo but not push 'deleted' directories and files back to origin/master 
the remote repo?

Please advise.

Regards.