This is an old revision of the document!
For example, if you are using the Global Inbox, this would be the “Local Folders” folder inside the “Mail” folder. Otherwise, it's a folder named after the mail server, inside the “Mail” folder. For example, “pop.gmail.com” if you're using gmail.
Tools → Account Settings → Server Settings → “When I delete a message”
In TB, select a top-level account on the left, then:
File → Compact Folders
Account Settings → Server Settings → Clean up (“Expunge”) Inbox on Exit
Preferences → Advanced → Network & Disk Space → “Compact folders when it will save over X MB”
Preferences → Advanced → General → Advanced Configuration → Enable Global Search and Indexer
Account Settings → (each account) → Junk Settings
Preferences → Security → Junk
Reset Training Data
can fix some problems and is global affecting all accounts.