As a subsequent answer to the call, you need to split these directories into different names or merge them correctly into the same name with the same name, depending on your needs, of course. They cannot have the same name in another case and work on Windows (in an explicit and obvious way).
I accidentally got into the same boat. I'm not sure how, when I used Windows all the time, but at some point I changed the case in the directory in the repo, and some files ended up in the directory with the old name, and some in the same with the "new" name. On my Windows machine, they were all under a new name, but I found this problem when I pulled out the repo on Linux and confirmed the split when I looked in my Assembla repository.
To fix this, I first cloned it to a separate location on my Windows machine. Thus, all the files were again in the same directory, since, apparently, the two directories are simply merged. Then I renamed this problem directory to "temp" (using the "rename" TortoiseGit operation). Then I cloned the repo to another place. At this point, the two directories were separated on Windows. I had "temp", plus a directory with the old name.
As I really wanted them in the same directory (on all platforms!), I moved the files from the old named directory to "temp" and then deleted the "old" directory. Then I renamed temp (again using the βrenameβ TortoiseGit operation) to the name in which I wanted everything inside, earned and clicked again. Finally, I put the changes into my original repo, my linux-one, and looked at Assemble. Everything was finally in agreement, so I deleted these temporary clones and called it day.
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