This helps fix linking issues and ambiguity related to the difference between classes and modules in FORTRAN 2003+.

Remove dependency of PLantUML on HAVE_DOT

Bug 738574 - … is replaced by \cdots rather than \dots in the LaTeX output

Bug 738548 - latex: dead links to source code

Updated configuration script and libdoxygen.pro.in to use llvm-config

Last comment of \code{.f90} missing

Package mathptmx gives discrepancy between pdf and HTML formulas

Seen the discussion with the pull request 229 the dependency of PlantUML and HAVE dot should be removed.

Changed the \cdots to \dots. Based on the bug report and on http://tex.stackexchange.com/questions/77737/dots-versus-ldots-is-there-a-difference

For Latex an extra dependency exists. In case Latex is set and LATEX_SOURCE_CODE is not set the writing of the "Definition in file" section is disabled.

This is needed on platforms like ubuntu 14.04 where several version of
clang can be installed, and the version is included in the location. The
best way is to use the llvm-config if available

Bug 738063 - Fortran attribute contiguous not identified

Empty entry in \tableofcontents in case e.g. section without description

Generate error message in case bibtex generation fails