I have been in similiar situations really often during my Bachelors (always fighting with different software plaftorms for sharing code - at the beginning of Bachelors, though - as we were not so advanced).
I was (like every other student) then introduced with the GIT and this is the thing that I would highly recommend!
If you, however, happen to have some merging problems, then just try using one of the following commands:
git fetch origin
git reset --hard origin/master

Good luck!

One such tool isĀ SourceTree, a free Git client for Windows or Mac. It provides an nice visual interface between you and Git, no more command line!

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