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I'm running Ubuntu on VM and MsysGit on Vista. I'm using Github as the git host and tracking the same repository from Msysgit too.

When I pull all the changes from Mysysgit and do the "git status", it lists the uncommitted changes. But when running "git status" from the Ubunutu, its all clean. No uncommitted changes.

Why is this happening in Msysgit. Both version is 1.6

+1  A: 

I had similar issue when I let MSysGit handle line endings. Currently I always install MsysGit with option not to convert line endings and commit them as they are.

Marcin Gil