doc: Reduce the validation errors of the docbook input

(this is different from previous version as it removes some
broken and irrelevant changes to the protocol appendix).

This removes all the validation errors except for missing link
targets. You can test this by removing the --skip-validation
from doc/publican/Makefile.am.

Main changes are to avoid nesting <para> commands. I also used
<simpara> in some places to reduce the amount of blank space.
And the reference id's are prefixed with the chapter name to
avoid collisions between libclient and libserver.

PS: it would be useful if somebody who actually knows something
about xslt would come up with a way to translate a block of text
makde of <para> commands unchanged, but add <para> around plain
text. Most of the difficulty is that doxygen's output is rather
inconsistent here.

Tested-by: Pekka Paalanen <pekka.paalanen@collabora.co.uk>