We're in the process of moving from Cyrus 2.4.17 to 2.5.7.

So far this is going OK - but I've noticed when I stop the 2.5.7 server
(this is on FreeBSD so 'service imapd stop') - it leaves behind idled?

Should this be stopped by the imap server itself, or does it need stopping
manually / by the control scripts?

I had this problem some time ago.
For me, solution was to use --with-libcap at configure/compile time. Linux here.

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master sends Term signal to all process group, including idled, although ppid 
is 1.

Problem here was that idled was being launched by root. So sending it a signal 
from cyrus user will not work.
Looking into code, I needed to add libcap "--with-libcap" to configure and 
recompile. This makes become_cyrus success before START section and idled being launched 
now by cyrus user.
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https://lists.andrew.cmu.edu/pipermail/cyrus-devel/2015-August/003393.html

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