Dovecot is configured to use:
sieve = /storage/mail/%u/.dovecot.sieve
but the managesieve plugin always writes its rules to:
/home/%u/sieve/managesieve.sieve
How can I change the location that the plugin reads and writes the ruleset to?
I figured it out. It is not the responsibility of the plugin to do this, but of the sieve server. For Debian using Dovecot I had it misconfigured and needed to change /etc/dovecot/conf.d/90-sieve.conf so that:
sieve_dir = /storage/mail/%u/sieve
and modify the sym-link at ~/.dovecot.sieve to point to the new sieve directory. User scripts are now stored in /storage/mail/%u/sieve and the symlink in the users home directory points to the active script at /storage/mail/%u/sieve/.dovecot.sieve. Useful documentation about Dovecot sieve is here:
http://wiki2.dovecot.org/Pigeonhole/Sieve/Configuration