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As was mentioned in #193 and on Matrix, every module needs to be changed to work with m.thread. I do not use all modules, and so I will let this PR sit here for a while. Please help test this if you can. It was tedious changing all the module calls, and while I was fairly patient in stepping through everything, there is a chance I've missed something.
Modules I use (sorted). Especially if you have one not on the list, please help test it:
alias
apod
bot
cron
echo
help
mumble
pt
rasp
room
users
wa