This probably is due to a change added in git-1.7.0 by which submodules become marked as dirty if they contain modified or untracked files.
git status
has an option --ignore-submodules
to ignore specific changes. From man git-status
:
--ignore-submodules[=<when>]
Ignore changes to submodules when looking for changes. <when>
can be either "none", "untracked", "dirty" or "all", which is
the default. Using "none" will consider the submodule modified
when it either contains untracked or modified files or its HEAD
differs from the commit recorded in the superproject and can be
used to override any settings of the ignore option in git-
config(1) or gitmodules(5). When "untracked" is used submodules
are not considered dirty when they only contain untracked
content (but they are still scanned for modified content).
Using "dirty" ignores all changes to the work tree of
submodules, only changes to the commits stored in the
superproject are shown (this was the behavior before 1.7.0).
Using "all" hides all changes to submodules (and suppresses the
output of submodule summaries when the config option
status.submodulesummary is set).
(this option was only added in git-1.7.2)