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After a conversation with Grok I discovered that since GnuPG 2.4.1 GnuGP on Windows may default to using the use-keyboxd option, which relies on a SQLite-based backend (pubring.db in ~/.gnupg/public-keys.d/) instead of creating a pubring.kbx file. See here and here.

In order to workaround this one can create an empty ~/.gnupg directory first or if a ~/.gnupg/common.conf file exists edit it so that
the use-keyboxd entry is removed or commented out like #use-keyboxd

If this becomes the default format going forward I wonder if this will be supported in BC/JGit?

Edit - see eclipse-egit/egit#12

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