Fixes #932: TODO tags did not show in marker report

The marker report with twig templates did not feature
TODO tags because these were never collected and
added to the marker index. XSL templates solved this
by using an, expensive, XPath query.

To solve this issue we have added a new compiler
pass that extracts TODO tags from all elements, adds
them to the marker listing and we have removed the
workaround from the XSL templates.
#1049: By reference was not passed from the Reflector to the Assembler

When an argument was declared as being 'by reference'
this was not registered on the Descriptor using the
Assemblers, and the XML writer did not set this in the
structure.xml.

During research it was also discovered that the
responsive template does not show calls by reference,
and probably the clean template not as well. This will
be addressed in a separate commit in the respective
repository.
#1049: Update changelog
Merge branch 'develop' of github.com:phpDocumentor/phpDocumentor2 into develop