title: Git mergetool on Windows keeps being given filepath from Git install rather than repository root
body: <p>I want to use SemanticMerge as my mergetool in Git, but when I try to perform a merge, I get a complaint from SemanticMerge saying that it cannot locate the file <code>C:\Program Files (x86)\Git\my_repo_name\my_project\MyFile.cs.BASE.1234.cs</code> - which is absolutely correct as it should be at <code>C:\repositories\my_repo_name\my_project\MyFile.cs</code> and so on. For some reason although Git is working with the repositories in every other respect, it seems to be determined to pass the $BASE, $LOCAL and $REMOTE file paths with the Git install path prepended instead of the repository root.</p>
  
  <p>I have been using the configuration suggested in <a href="http://rlbisbe.wordpress.com/2013/04/15/semantic-merge-as-the-default-merge-tool-with-git-on-windows/" rel="nofollow">their own tutorial</a> as a starting point for this and the tool seems to work fine if given the correct paths, so I am guessing that somewhere between Git and MsysGit, there is some misconfiguration or miscommunication.</p>