Sorting the mail folder list
Default sort order
By default the mail folder list in the left pane contains top-level nodes in the following order:
On This Computer - contains all mail for local account types (if configured)
One or more remote email account types (if configured)
Search Folders (if enabled)
The folders under each top-level node are sorted in alphabetical order.
Changing the sort order
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You can change the default sort order of the top-level nodes under Edit ▸ Preferences ▸ Mail Accounts by dragging an account in the list up or down.
You can revert your custom sort order by choosing Edit ▸ Preferences ▸ Mail Accounts ▸ Restore Default.
You can change the sort order of folders under Folder ▸ Edit Sort Order….