On Travis, the build directory '/home/travis/build/cantera' matched the (no
longer needed) exclude pattern of ' /build/*', causing all source files to be
skipped.
The files kinetics.h and onedim.h are present as high-level application
include files and as lower-level implementation include files. Doxygen
generates HTML documentation for all files in the same folder, and on
case-insensitive file systems, the documetation for the application and
the implementation files will shadow each other. This commit enables the
option to put documentation files into subfolders in the root directory,
hopefully separating these "duplicate" files
This is needed to make MathJax work when loading the documentation over an https
URL, since some browsers block scripts from non-https sites when loading a page
over https.
This also fixes a bug where jquery.js was not being copied to the directory with
the generated documentation on some operating systems (Debian-based Linux
distributions).
As of Doxygen 1.8.0, documentation for inherited member functions is listed in
an expandable section of the derived class's documentation, which seems like a
better compromise.
