I saw this problem in Windows (not Linux) running the msysGit bash prompt


git submodule update

error: Entry 'README.rdoc' would be overwritten by merge. Cannot merge. Unable to checkout 'fee9487e0d5464fc328f1c9c91eb059fef75988e' in submodule path

Change directories to submodule path and run this to fix it


git reset --hard master

Also grab this iRC client for Windows: http://www.xchat.org and go to the #git channel on the FreeNode server for a lot of good git discussion. This is where I figured out this problem

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