Are you sure you're using direct mode? I see many indications your repository contains lots of symlinks, which would suggest it's in indirect mode.
Do any of these files have the same contents? In particular, I suspect one of them, and probably all of them are empty. vboxshare/Web Platform Installer/webpi_launcher_log.txt archive/puc/cursos/2010-1/Taller/software/lib/vendor/symfony/test/unit/util/fixtures/finder/FILE5.txt archive/puc/cursos/2010-1/Taller/software/lib/vendor/symfony/test/unit/util/fixtures/finder/file2.txt See http://git-annex.branchable.com/bugs/Handling_of_files_inside_and_outside_archive_directory_at_the_same_time/ -- see shy jo
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