Bug 724949 - Server side (PHP) search broke in 1.8.3
Added dir tree nodes to the context
Unified DirFileContext and NestingContext
Added directory info to the context
Extension in config.xml if type=string with format=image

In case of a project logo a preview is shown in the "wizard mode". In "expert mode" only the name is shown.
In this patch the config.xml the type=string possibilities are extended with format=image (config.xml, configgen.py, config.h).
The doxywizard has been extended so that in "expert mode" this type is supported and that a preview is given (expert.cpp, inputstring.cpp and inputstring.h), furthermore in wizard.cpp a minimum label size has been defined to prevent jumping of the items in case of switching between a message text and an icon.
In case of sections with the same name they are not reported.

In this patch it is checked if a section label has been used before and if so a warning is given with file name and line number (when possible) where the section label was used the first time.
Note in section.h the item level was not initialized in the past in case of a copy constructor.
Extension specific filtering
pass libclang header file location; add paths for Ubuntu's llvm-3.4
Bug 625601 - FORTRAN: recognition free versus fixed formatted code

The recognition of the type (free or fixed) of Fortran code is not reliable possible. A well known possibility as used with compilers as well is to specify the type of code by means of the extension.
With EXTENSION_MAPPING it is possible to select the type of Fortran code, when not explicitly set doxygen tries to guess the type of Fortran code.
Bug 643618 - Fortran: variable with name "type" confuses Doxygen

Most problems were solved in version 1.8.5 but the underscore character (_) had not been incorporated, this is done with this patch.
Alterative way to get rules information from flex

This patch describes an alternative way to get rules / debug information from flex files
Added reference counting for all context objects
Merge pull request #136 from albert-github/feature/bug_doc_arch_lex

Alternative way to get rules information from flex
Merge pull request #135 from albert-github/feature/bug_643618

Bug 643618 - Fortran: variable with name "type" confuses Doxygen
Merge branch 'master' of github.com:doxygen/doxygen
Merge pull request #131 from albert-github/feature/bug_725516

Bug 725516 - In case of sections with the same name they are not reported.
Merge pull request #132 from mr-c/clangfix

pass libclang header file location; add paths for Ubuntu's llvm-3.4
Merge branch 'feature/bug_625601' of https://github.com/albert-github/doxygen into albert-github-feature/bug_625601
Some restructuring and some compiler warning fixes
Merge branch 'master' of github.com:doxygen/doxygen