One arguably strange behavior in MailMate is that when you archive a message, other messages in the thread can stay in your inbox.
Fortunately, it's possible to re-map the archive keyboard shortcut to archive all messages in a thread. Using the instructions for adding custom keybindings, add the following:
"y" = ( "selectWithFilter:", "#thread-id = ${#thread-id}", "archive:");
Note that I use "y" instead of "e" because I use FastMail instead of Gmail.
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