Using SourceTree on Mac I just cloned a repository to a Samba mounted Linux drive. Immediately SourceTree showed a file as having pending changes. SourceTree isn't suggesting these are EOL changes, but actual edits introducing additional code. I attempted to discard the file, but it simply never disappeared from showing as pending in SourceTree.
On the Linux machine, git from the shell showed a different git status. 'git status' showed the file SourceTree thinks had a few minor changes as having been 'deleted'. git status also showed several other files as having 'typechange'. Performing a 'git reset --hard' within Linux reset it so that 'git status' reports back "Your branch is up-to-date... nothing to commit, working directory clean".
However, back in SourceTree things have now gotten worse. Now SourceTree is reporting the original report of a changed file, plus a tonne of files as being untracked, some deleted and a few more as also having changed.
I deleted the entire repository and did a fresh clone and SourceTree ended up right back where I started - incorrectly reporting the status of the repository.
When I've seen behavior like this, it's because there have been files present in the source repo whose names differed only by case (i.e. foo.bar and FOO.BAR exist in the same directory). By default, Macs will not allow file names to differ only by case (and this behavior is also standard on Windows computers). Therefore when the clone operation occurs, only one or the other of the files will get copied onto the Mac. But git knows that both files are supposed to be there. It may show one as deleted or it may show that the contents of one have changed (to the other).
The best solution is to not have files whose names differ only by case in your repo. This will give you the best compatibility when people clone to workstations. It's also possible to put your Mac into a mode where it will allow files that differ only by case (the same way linux will) - you can google for that, I don't know the steps off the top of my head but I know it can be done. But then you'd still have this issue if you had a developer clone onto a Windows PC, so I think it's best to just fix the filenames on your remote repo. You'll have to use a unix workstation that you can clone the repo to in order to fix the names.
This is all assuming that I'm right about the source of your problem - but I bet I am.
Windows machines also have restrictions on files ending in a period or with certain special non alphanumeric characters in them, by the way, so it's best to avoid these also for maximum workstation compatibility.
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