doc: Organize Doxygen documentation in logical groups

Signed-off-by: Alexandru Gagniuc <mr.nuke.me@gmail.com>
doc: Update protocol description for parsing by Doxygen

The protocol itself is not changed, only the markdown structure so that
Doxygen can properly parse it to HTML.

Signed-off-by: Alexandru Gagniuc <mr.nuke.me@gmail.com>