Git Management: Single Git at root directory where the files are residing in other directories

Hi

I have setup a development server and developers will develop the codes in their local machine.

In the development server, there is a Git Repository at the directory, S1:\main\. I read that having a single consolidated Git Repository is better than having multiples Git Repositories lying around the system.

For each project, the python files will be at a subdirectory ie S1:\main\projectA\python\  or S1:\main\projectB\python\. The Git will have a develop (main branch) , Tom's branch, Henry's branch.

Each developer, will pull the python files from the "develop branch" and work in his own local machine. He will have a Git Repository and all his python files will be at the same location C:\ProjectA\  

If I create a new file in my C:\ProjectA\ and push it to the "develop branch" and perform a merge at the "develop branch", the file is located at S1:\main\ instead of S1:\main\ProjectA\python\. If I manually cut and paste the file from S1:\main\ into S1:\main\ProjectA\python\, the Git will give me the following error: "Git Merge Failed Your local changes would be overwritten by merge. Commit, stash or revert them to proceed"

How do I put the python files at the right directory in the development server so that my local Git can link up with the Development Server's Git?

Thanks