You're right, using exclude rules is the Subversion way of disabling tag indexing. For git, there is no option in the admin UI to disable tag indexing, but you can add the --Xdisable-tags flag to the FISHEYE_ARGS environment variable to disable tag indexing for DVCS repositories. This flag controls both git and mercurial repositories.
You could try to add Exclude rules, as they allow you to exclude files and directories from those which have been included in indexing. FishEye will not process these files and directories.
Please see this document for more information:
And please feel free to contact Atlassian Support if you have any problems while doing this.
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