Cross platform way to manage a project (and git/github)

I have a cross platform python package and push them from pycharm to github directly. For ease of maintaining the project locally, I have kept the source code in a separate directory/drive accessible to both Linux and Windows. The source directory is already added to git/github. All I need is to log in to Windows or Linux and keep working on the same source code. However, every time I login to different OS, the colour of these files (git indicative of change in the file) keep on changing. I am unable to figure out which file I modified last and need to commit/push to remote repo.

My question is, what is the correct cross platform way to manage a local repo and git integration under PyCharm? Or is it really a bug?
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I'm guessing this has to do with filesystem metadata being different between the systems over a network drive. Honestly, I would not recommend trying to share a single git working copy over a network share. I would just make separate working copies on each system. That's how git is designed to work.
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Excuse me , I have a small issue. Noot really related to this area of the forum but I'm sure you can help actually?

Im scripting in python using pycharm and I am unsure where to save my modules at so that in the python console I cam import them for usage. please help many thanks to you.
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Thanks for the reply.
I do suspected the same issue. I do not share a single git working copy over a network share. It is just a directory accessible to both operating system.

How do avoid such an error or what is the correct way of maintaining a single local repository for cross platform development?
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Are you dual booting Windows / Linux on the same PC and switching back and forth? Or using something like Dropbox to sync a folder? Otherwise I don't really understand how it can be a directory accessible to both operating systems and not be a network share. If you are running one as a virtual machine inside the other and sharing folders, that operates as a network share.
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Yes I am dual booting Windows and Linux.
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