man/*: formatting cleanup

Fix some problems with indentation (controlled by markup) and
whitespace.

- notmuch.1: reformat

  Use .SS macro to make "notmuch setup" a subsection. Introduce another
  subsection for the remaining commands.

- notmuch-config.1: reformat

   Put all the syntax in the synopsis. Supposedly this is the the UNIX way.

- notmuch-reply.1: fix formatting issues.

  Give nicer formatting for synopsis.

  Insert missing SEE ALSO header.

- notmuch-dump.1: reformat using subsections

  These seems more natural, although, as mentioned, it does require
  referring back to the synopsis. Or maybe copying parts of the
  synopsis