How to get rid of duplicate msgs?
Use the "~=" mutt-pattern (manual.txt section 4.2) to delete or tag them. Beware: in old versions this pattern works only when you sort the folder by "thread".
How to change the order within a thread?
How to sort threads based on all the messages in the thread?
RTFM sort_aux, it controls not just the order of messages within each thread, but also the order of threads themselves!
A good use for this is:
so that threads with messages received recently will show up later in the index (by default threads are sorted based on the first message in the thread).
Why are some msgs threaded and others not?
You have some msgs which don't have correct
headers (or not set at all) and you've turned on
What do "->", "-?-" and "*>" mean in thread trees?
When you turn off
msgs with similar subjects get grouped together. In those threads "->" indicates real threads (by the above mentioned headers) and "*>" indicates pseudo threads (by subject only).
"-?-" indicates a referenced msg, which is missing in the current folder.
Why is the tree display screwed, I see garbage chars in front of the arrows?!
Try setting $ascii_chars on. If the display is still messed up, then you have a problem (i.e. flea). Otherwise the fancy tree chars resulted from a bad combination of your used terminal emulation and/or wrong $TERM setting in the shell, or maybe even $LC_CTYPE or $LANG (see "man locale"). See MuttFaq/Charset.