tools/pyboard.py: Change logic for when raw ">" prompt is parsed.

In raw REPL ">" indicates the prompt.  We originally read this character
upon entering the raw REPL, and after reading the last bit of the
output.  This patch changes the logic so the ">" is read only just
before trying to send the next command.  To make this work (and as an
added feature) the input buffer is now flushed upon entering raw REPL.

The main reason for this change is so that pyboard.py recognises the EOF
when sys.exit() is called on the pyboard.  Ie, if you run pyboard.py
with a script that calls sys.exit(), then pyboard.py will exit after
the sys.exit() is called.