Added a comment: One possible workaround
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[[!comment format=mdwn
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username="EvanDeaubl"
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avatar="http://cdn.libravatar.org/avatar/00804f84646da416472678b573fd9d30"
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subject="One possible workaround"
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date="2021-02-22T16:23:40Z"
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content="""
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I ran into this exact situation trying to split content across multiple repos by directory, and ran into a couple of files with many duplicate keys throughout the repo. I worked around it by applying a tag to the offending key, and including that tag as part of the preferred content expression:
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```
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git annex metadata -t common-signature $FILE_WITH_DUP_KEY
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git annex wanted . 'include=\"foo/*\" or include \"bar/*\" or metadata=tag=common-signature'
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```
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This would result in a file possibly being included in a repo where it wouldn't be otherwise (if it wasn't in one of the include directories to begin with), but in my case, the common files were few and small (2, both less than 100K).
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"""]]
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