Support for explicit include files

Instead of using links to other source directories
we now use explicit include files. The approach is more
robust.

Closes #69
Improved makefile

Needed to have proper regeneration of links when new .h files are added.
I also added several comments.
Updated developer Doxyfile to latest doxygen version
Improved developer Doxyfile

I removed many graphs that were probably not useful
and were cluttering the output. Moreover, I
enabled the search engine and added an alphabetic
list of classes (classes -> class index)
New user doxyfile

I updated doxyfile to latest doxygen version. I also
enables the search engine. This required a small fix on the
extract script so that "action" pages receive a proper name
for the index.
Merge branch 'v2.0'

Conflicts:
	user-doc/extract

    A large portion of extract was rewritten on master,
    I just redid the change I did on fix-69
changelog
Merge branch 'v2.0'