Git not uploading all files

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Hi, i have setup my server using the instructions from :
http://danbarber.me/using-git-for-deployment/
I have a bare repo thats pushing changes to web . It work ok, except for
some issues.
I noticed that some files were not uploades, although they look fine
according to gitweb:

261 files changed:
www/sites/all/modules/contrib/jquery_update/CHANGELOG.txt	[new file with
mode: 0644]	blob
www/sites/all/modules/contrib/jquery_update/LICENSE.txt	[new file with mode:
0644]	blob
www/sites/all/modules/contrib/jquery_update/README.txt	[new file with mode:
0644]	blob

I notice that in /var/www i did not have the jquery_update folder or any
files within that folder. The path was not included in .gitignore and all
other files were uploaded fine.
I checked the logs on server and nothing happenned at that time , no errors
from server.

Do you have any ideeas why this could happend? 

Thank you
Andy

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