The separate git dir feature was added for issue SRCTREEWIN-402 I had reported for 0.9.0.5. I just upgraded to 0.9.1 and can now add my existing repositories. However when doing a 'pull' operation I get an error result with:
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git -c diff.mnemonicprefix=false -c core.quotepath=false fetch origin

git -c diff.mnemonicprefix=false -c core.quotepath=false pull origin master
From d:/rio

• branch master -> FETCH_HEAD

Already up-to-date.

git -c diff.mnemonicprefix=false -c core.quotepath=false submodule update --init --recursive
You need to run this command from the toplevel of the working tree.

Completed with errors, see above.
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The setup has the normal repository in d:\rio and the separate-git-dir respository in d:\rio-export. (used to pull the current version and then zip the tree so I have the .git directory outside that tree)

I get the above messages when doing a pull into the master branch rio-export from the master branch of rio. The same operation works normally with TortoiseGit.