notmuch.el: Indent messages to show nested structure of thread.

Now that we're actually adding text to the buffer for the indentation,
our old aproach of using positions to record regions to manipulate is
now longer correct. Fortunately, it's easy to switch from positions to
markers which are robust, (just call point-marker instead of point and
all relevant functions accept markers as well as points).

I also finally fixed the bug where the text "[6 line signature]" we
display was causing the one-line-summary of the next message to be on
its same line rather than at the beginning of the next line where it
belongs.