HUGE Refactor AbstractMarkupFilter and YAML config PR now ready....

[jim]

This is a big one - even for me :-)

I focused on finally doing a refactor of AbstractMarkup filter. We were
not properly tracking extraction state and many things weren't working
like preserve whitespace, embeddings of
INCLUDE/EXCLUDE/INLINE_EXCLUDE/INLINE_INCLUDE. Also in several cases
conditions where not checked and a rule applied when it shouldn't have.
All end tags now must be matched with a start tag to get the full
extraction state (in all wellformed cases).

The logic is not simpler per se, but is more consistent and should be
easier to follow with fewer exceptions like clarifyPreserveWhitespace etc..

I had to comment out some code in the integration tests for comparing
target content - but this is failing because of TextUnitMerger - which
is my next task. I don't want to fix that in this PR.

Jim