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[[!comment format=mdwn
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username="joey"
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subject="""comment 3"""
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date="2019-03-22T13:25:22Z"
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content="""
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annex.thin will only make one hard link to a given annex object file, so if
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the file that is not getting hard linked has the same content as another
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file in the repository that is getting hard linked, that explains why.
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It would be very susprising for two different files in the repo to end up
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hard linked together and then a modification to one change both files.
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You should really upgrade to git-annex 7.x when using v7 mode. You
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are both using versions that are missing quite a lot of the fixes needed to
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get v7 to release quality.
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So please upgrade to a current version and see if your execute bit problems
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persist there.
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"""]]
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