Cloning from a repository with a subtree corrupts the directory holding the subtree

[tonnydourado]

I was trying to clone a repository (hosted through JGit, just in case it matters) that has a subdirectory with a subtree. When I clone the repository, the directory gets corrupted, turning into a file with no permissions, not even reading. This causes other operations, like pull, to fail because they can't open that file. Here's the traceback from trying to pull, because cloning doesn't raise any errors (I anonymized the names just in case, it's a internal project):

In [20]: repo.pull(origin_uri='http://192.168.0.42/repository')
---------------------------------------------------------------------------
IOError                                   Traceback (most recent call last)
<ipython-input-20-c27ea9c87ec2> in <module>()
----> 1 repo.pull(origin_uri='http://192.168.0.42/repository')

/usr/local/lib/python2.7/dist-packages/gittle/gittle.pyc in pull(self, origin_uri, branch_name)
    358     # Like: git pull
    359     def pull(self, origin_uri=None, branch_name=None):
--> 360         return self.pull_from(origin_uri, branch_name)
    361 
    362     def fetch_remote(self, origin_uri=None):

/usr/local/lib/python2.7/dist-packages/gittle/gittle.pyc in pull_from(self, origin_uri, branch_name)
    354 
    355     def pull_from(self, origin_uri, branch_name=None):
--> 356         return self.fetch(origin_uri)
    357 
    358     # Like: git pull

/usr/local/lib/python2.7/dist-packages/gittle/gittle.pyc in fetch(self, origin_uri, bare, origin)
    420         # Checkout working directories
    421         if not bare and self.has_commits:
--> 422             self.checkout_all()
    423         else:
    424             self.update_server_info()

/usr/local/lib/python2.7/dist-packages/gittle/gittle.pyc in checkout_all(self, commit_sha)
    733         commit_tree = self._commit_tree(commit_sha)
    734         # Rebuild index from the current tree
--> 735         return self._checkout_tree(commit_tree)
    736 
    737     def checkout(self, ref):

/usr/local/lib/python2.7/dist-packages/gittle/gittle.pyc in f(self, *args, **kwargs)
     45     def f(self, *args, **kwargs):
     46         assert self.is_working, "%s can not be called on a bare repository" % method.func_name
---> 47         return method(self, *args, **kwargs)
     48     return f
     49 

/usr/local/lib/python2.7/dist-packages/gittle/gittle.pyc in _checkout_tree(self, tree)
    726             self.repo.index_path(),
    727             self.repo.object_store,
--> 728             tree
    729         )
    730 

/usr/local/lib/python2.7/dist-packages/dulwich/index.pyc in build_index_from_tree(prefix, index_path, object_store, tree_id, honor_filemode)
    439                     raise
    440         else:
--> 441             f = open(full_path, 'wb')
    442             try:
    443                 # Write out file

IOError: [Errno 13] Permission denied: '/tmp/repo/subtree-directory'

We ended up deciding to just remove this subtree: it's unused code anyway, and it only happens on one repository. However, I'm opening the issue just to register the problem. I can try to run some more tests if you guys need more data, but I can't give you the original offending repository for the reasons stated before.