On Tue, Sep 17, 2013 at 5:46 AM, Martin Gregory
<martin.greg...@adelaideinterim.com.au> wrote:
> An additional note.  I did
> git ls-files -v | grep ^S
> and I can see that the files that remain in the working version have the ^S
> bit set.
> So it does feel like a bug to me: why are files with ^S set remaining in the
> working version after
> git read-tree -mu HEAD
> ?

I don't know. Maybe the bits are set, but then the remove operation
fails (silently). I tried to reproduce on Linux without success. It
seemed to work ok. Can you copy the (stripped down if necessary)
repository somewhere? Pack the whole thing including worktree and
config file, just in case.
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