Removed functions at(), set() and add(), everything (and more) can be
now done using operator[]. Accessing matrix elements is now done through
column vectors, e.g.:
Matrix4 a;
a.at(row, col); // before
a[col][row]; // now
Note that because operator[] on Matrix returns column vector (there is
nothing like row vector), the parameter "order" is now swapped.
All HTML code and Doxygen shortcuts such as @c, @b and @em are now
rewritten using Markdown syntax, which makes it more readable.
Also updated Doxyfile. Doxygen 1.8 at least is required to generate
the documentation now.