v1.11.1
For any people who've been affected by libgit2/libgit2#2085 (comment) (git fsck will show error in tree xxxxxxx: contains duplicate file entries in affected repos) - this latest release of The BFG adds a switch to make removing the duplicate tree-entries easy:
$ bfg --fix-filename-duplicates-preferring tree
I've tested this against a copy of the corrupted CocoaPods/Specs repo, getting a clean git fsck in just over 2 minutes.