This bug isn't present in darcs 2.1.0 and is present in latest HEAD.
Haven't had time to check inbetween yet.

issue1612 may be related but is reported as being present at least from
darcs 2.0.2 

darcs init
mkdir dir
touch dir/file

darcs add dir/file              # adds dir too (which is fine)
darcs rec -a -m"add dir and file"

darcs remove dir
darcs rec -a -m"remove dir"     # doesn't remove file!

darcs obliterate -a --patch "remove dir"
darcs check

Test case pushed.

Also, note that the bug doesn't manifest for old-fashioned repos,
because darcs record tries to remove the directory from pristine and fails.

It's great that we have this pinned down, not only to a test, but to a
lower bound version.  Looks like we may have some luck tracking this one
down (marking ThePendingPatch topic because this bug may be about
putting silly things in pending, but then again, the fact that this does
not appear in old-fashioned is odd)

Oh, I didn't read your report carefully enough.  If I had done so, I
would have seen your explanation for why it does not manifest in
old-fashioned repos.

I've now verified that this bug isn't present in 2.3.1

Since this is (a) a repo corruption issue and (b) a regression over our
last release, I think it should block the current release. Sorry, Reinier!

BTW I've now confirmed that this is present in the 2.4 branch as well as
HEAD.

I plan to track down how this was introduced and fix it as soon as
possible (next few days) but obviously any input from anyone else in the
meantime would be welcome.

This was resolved by Reinier for the 2.4 release, but I never got around
to fixing my staging repo, so the automatic bug resolver never triggered

The following patch updated the status of issue1749 to be resolved:

* resolve issue1749: refuse to remove nonempty directories in makeRemovePatch 
Ignore-this: ad57e75a8f336ca97a981e16933a74ea