Package mathptmx gives discrepancy between pdf and HTML formulas

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.
Last comment of \code{.f90} missing

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

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 738548 - latex: dead links to source code

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.
Bug 738574 - &hellip; is replaced by \cdots rather than \dots in the LaTeX output

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
Remove dependency of PLantUML on HAVE_DOT

Seen the discussion with the pull request 229 the dependency of PlantUML and HAVE dot should be removed.
Added faster reference counted string implementation with short string optimization
Merge pull request #232 from albert-github/feature/problem_mathptmx

Package mathptmx gives discrepancy between pdf and HTML formulas
Merge pull request #237 from albert-github/feature/bug_fortran_codecomment

Last comment of \code{.f90} missing
Merge pull request #238 from frosteyes/master

Updated configuration script and libdoxygen.pro.in to use llvm-config
Merge pull request #239 from albert-github/feature/bug_738548

Bug 738548 - latex: dead links to source code
Merge pull request #240 from albert-github/feature/bug_738754

Bug 738574 - &hellip; is replaced by \cdots rather than \dots in the LaTeX output
Merge pull request #242 from albert-github/feature/plantuml_dependencyfeature2

Remove dependency of PLantUML on HAVE_DOT
Fixed refcounting bug in new string implementation
Merge branch 'master' of github.com:doxygen/doxygen
Added clearer range checks for string class to help compiler
Reverted back to old string implementation. New one needs more work.
Added compilation support for MacOSX 10.10 (yosemite)
Introduce new optimized string implementation (attempt 2)
Initialized potentially uninitialized variable in markdown part