the usr/share/repligard one is installed by midgard-data, /var/lib/aegir is part of the aegir_dirs package. The one repligard will use by default is the one installed by midgard-data (the files are propably identical save for usernames and passwords).
Weird. Most recent versions of midgard-data have been installing the repligard files in /usr/local/etc on my system. Difference in platform, perhaps? I'm using Dead Rat 8.0, maybe others are using a different distro.
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