This leads to a java.lang.StringIndexOutOfBoundsException if I rename a project which has a repository in the project folder and which is located outside the eclipse workspace. In this case the location does not change. 

This error had been there before. I think it is the same as was reported in comment 2 of bug 334112. Mabe we could fix it in another change, but you could mention it in the commit message as a further limitation.