[[!comment format=mdwn
 username="joey"
 subject="""comment 4"""
 date="2018-07-17T14:59:26Z"
 content="""
Looking at those files, all the duplicated files
are located at least 2 subdirectories deep, and most more like 5-7
deep. But, almost all of the repo is inside such
subdirectories, so that is not conclusive.

Aha! I managed to reproduce it:

	joey@darkstar:~/tmp/t#master(unlocked)>mkdir ook
	joey@darkstar:~/tmp/t#master(unlocked)>cd ook
	joey@darkstar:~/tmp/t/ook#master(unlocked)>mkdir boop
	joey@darkstar:~/tmp/t/ook#master(unlocked)>cd boop
	joey@darkstar:~/tmp/t/ook/boop#master(unlocked)>mkdir beep
	joey@darkstar:~/tmp/t/ook/boop#master(unlocked)>cd beep
	joey@darkstar:~/tmp/t/ook/boop/beep#master(unlocked)>mkdir yeep
	joey@darkstar:~/tmp/t/ook/boop/beep#master(unlocked)>cd yeep
	joey@darkstar:~/tmp/t/ook/boop/beep/yeep#master(unlocked)>date > X
	joey@darkstar:~/tmp/t/ook/boop/beep/yeep#master(unlocked)>git annex add
	add X ok
	(recording state in git...)
	joey@darkstar:~/tmp/t/ook/boop/beep/yeep#master(unlocked)>git annex sync
	commit
	[adjusted/master(unlocked) fe11872] git-annex in joey@darkstar:~/tmp/t
	 1 file changed, 1 insertion(+)
	 create mode 100644 ook/boop/beep/yeep/X
	ok
	joey@darkstar:~/tmp/t/ook/boop/beep/yeep#master(unlocked)>git fsck
	error in tree a5fcd5b3aa5189ed8916f025cf035fce74098a1a: duplicateEntries: contains duplicate file entries
	Checking object directories: 100% (256/256), done.

Ok, it seems it's simply caused by deep paths in the tree and nothing
else. Will debug from here.
"""]]
