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/usr/share/doc/atheme/VERSION_LETTERS is in atheme-services 7.2.9-1.

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Letters in version responses
----------------------------

Version replies (from /version or ctcp version) contain a sequence
of letters like FljR. Their meaning is as follows:

A - ASCII casemapping is used
a - external authentication is used
c - an encryption module is loaded
d - debug logging is enabled
e - nick/account registration requires email verification
F - flood checking is enabled
l - leave_chans is enabled
j - join_chans is enabled
t - changets is enabled (shown as of 2.1)
R - RFC1459 casemapping is used
r - operserv raw can be used
n - services is attached to a terminal
T - services is tainted (running an unsupported configuration)