I ran into the same problem as Peter, and you're post was very helpful John.  Thanks for the workaround!

Lance

Peter Cock wrote:
On Thu, Apr 11, 2013 at 5:02 PM, John Chilton <chilton@msi.umn.edu> wrote:
Hey Peter,

  Hopefully Nate will have some wisdom, all I have is a workaround (I
have fought with this on multiple forks and this is the best I have
come up with).

Check out a clean version of the tools branch somehow (it seems like
the working contents can get stuck in an invalid state that update and
checkout cannot recover from). Once you are back to a good state, it
works when you merge in two steps.

hg checkout tools
hg merge -r ee389d2
hg ci -m "Partial merge."  # Not sure if this step is needed.
hg merge default

-John

I don't understand quite what it is doing, but it seems to have worked
on a quick test repository (I re-cloned Galaxy and my fork on bitbucket).
I've not just push any of these changes to bitbucket - they're all still
local to this experiment for now.

Unless I hit an issue or Nate has some alternative recommendations,
I'll probably do this tomorrow (its home time here in the UK).

Thanks John,

Peter
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--
Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
Princeton University