Those are part of Moodle core ... don't think they are available via download sepearately.
Check your Moodle code folder (moodle) /filter for a folder called data and a folder called glossary as well as moodle/admin/tool/assignmentupgrade
Hard to see the 'red' in your screen cap but looks like mod_glossary and mod_data and mod_asign 'collapsed'. Are those special mod's?
If those were among the items pulled when issuing git pull, then they might be tagged as belonging to 'root' user.
Fix while in the moodle directory: chown apache:apache * -R
That means all files and -R is recursion ... all files/folders contained there in. No need to restart apache, just reload the page.
If they are missing, then one could git clone moodle again to another directory (could be anywhere ... doesn't have to be in web document root):
git clone git://git.moodle.org/moodle.git moodlegit
git branch --track MOODLE_23_STABLE origin/MOODLE_23_STABLE
git checkout MOODLE_23_STABLE
chown apache:apache ../moodlegit -R
Then cp the *missing folders* to appropriate locations in the production server. cp -rp [folder] [to_production_moodle_folder]
cp -rp /var/www/moodlegit/filter/data /var/www/html/moodle/filter/
and so for the others as well. cp copy -r recurse the 'p' means preserve permissions/ownerships first path location of folder to copy last path location to copy to.
'spirit of sharing', Ken