Here is the problem:

=========================
:~/tmp/darcs> darcs --version
1.0.8 (release)
:~/tmp/darcs> ls
:~/tmp/darcs> darcs init
:~/tmp/darcs> mkdir dir
:~/tmp/darcs> darcs add dir
:~/tmp/darcs> darcs query manifest
:~/tmp/darcs>
=========================

As you see, the folder "dir" is actually managed by darcs, but is not shown in
the manifest.

Check out 'darcs help query manifest' and notice that
--no-directories is the default.

Works with darcs query manifest --directories (as Tommy pointed out).  On the
other hand, it might be fair to say that this should the default, not the other
way around.

> other hand, it might be fair to say that this should the default, not the other

This was suggested when the manifest command was implemented.

Ian Lynagh:
| Default to listing everything is probably simplest.

Florian Weimer (implementer of the manifest command):
| Usually, a manifest file does not list directories, doesn't it?
| Therefore, I've made --no-directories the default.  But I can change
| this easily.

Simplicity and least-surprise are of course good reasons for
changing it, but there have not been a great deal of reported
surprise (compared to other things with darcs that we have
changed because of that reason), and there might be users who
think that manifest generating a "normal" manifest is simpler. I
don't use the command myself so I don't have a strong opinion,
but maybe we should propose such a change on the user mailing
list first.

Just to follow up, the advice on darcs-users has been to rename 'query manifest'
to 'list files' (query is retained as alias for list; and manifest as an alias
for files).  List files will show directories by defaults; manifest will retain
the old behaviour.

Will submit a patch for comments.

Resolved in unstable with the following patches.  Thanks!

Tue Jul 17 00:03:08 CEST 2007  Eric Kow <eric.kow@loria.fr>
  * Make --directories the default in query manifest (issue456).

Wed Jul 18 22:47:03 CEST 2007  Eric Kow <eric.kow@loria.fr>
  * Rename query to list; manifest to files.
  
    query          => list (with query as alias)
    query manifest => list files (with manifest as alias)
    query tags     => list tags
  
  Note that the list manifest and list files commands differ in that the
  former displays directories by default and the latter does not.

The naming of the commands is still not settled, but we're working on it
(darcs-users).