In LaTeX 2 consecutive single quotes are joined to 1 double quote. This leads in texts where 2 single quotes are intended to a strange view. An example is the initial value for variables. E.g. in Fortran: character(len=10) :: A = ''  (i.e an empty string which can either be defined as '' or as "") or in C: char *sq  = "''". In the source listings this is OK but in the description text it was not OK.

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

In case e.g. an number of Fortran variables are documented as an example in a \code block and the last line looks like:
INTEGER :: var !< documentation
The "!< documentation" is missing as the last block was not rendered.
Note: STRIP_CODE_COMMENTS has to be NO as otherwise the code comment will anyway, correctly,  be absent.

Added keywords contiguous and volatile

In case a section, subsection etc just has a tag and not a description in the \tableofcontents there is nothing mentioned. With this patch the tag is used as description when no description is present, as is done on other places as well (consistency and no empty items in the \tableofcontents).

In case bibtex fails no message is given. When perl is missing the OS just emits an message. With this patch doxygen logs a message (analogous to other calls to portable_system)

When using the mathcal command in formulas the mathptmx package gives in the different output version different letters.
When the mathptmx, more exuberant,  type of fonts are to be used they can be added by means of the EXTRA_PACKAGES option for the dot version.