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When editing mailbox from edit-mailbox.php, aliases are not taken in account and it leads to misconfigurations (alias remains active but mailbox not or vice versa).
I'm attaching a patch that I've used in my installation.
Thanks for your patch! I commited it to the 2.3 branch (r1479) - if we do a 2.3.7 release, it will contain the fix.
SVN trunk (which contains a complete rewrite) already has this fixed since some time.