This patch is a patch for the build system so that less (no) generated files are in the source directories and also that the different build (on windows are independent of each others). Also the different sub-projects (e.g. doxygen , doxywizard) don't share any files anymore.

- ./.gitignore
  A number of files are not in the src directory anymore. generated directories are included. rtf and xml directories are there for possible future use.

- ./Doxyfile
  The generated files are not anymore in the src directory so they don't have to be excluded anymore

- ./configure
  Adjustmenst so the generated files are in the different subdirectories

- ./Makefile.in
- addon/doxmlparser/examples/metrics/metrics.pro.in
- addon/doxmlparser/src/doxmlparser.pro.in
- addon/doxmlparser/test/xmlparse.pro.in
- addon/doxyapp/doxyapp.pro.in
- addon/doxysearch/doxyindexer.pro.in
- addon/doxysearch/doxysearch.pro.in
- addon/doxywizard/Makefile.in
- addon/doxywizard/doxywizard.pro.in
- libmd5/libmd5.pro.in
- qtools/qtools.pro.in
- src/Makefile.in
- src/doxygen.pro.in
- src/libdoxycfg.pro.in
- src/libdoxycfg.t.in
- src/libdoxygen.pro.in
- src/libdoxygen.t.in
  Adjustment to the new directory structure

- addon/doxywizard/expert.cpp
  include file is generated in the generated_src/doxywizard directory, referenced through -I on compile line

- src/lang_cfg.h
  File is now automatically generated

- src/languages.py
  Correction of used path for new structure

- src/settings.py
- src/version.py
  Place for resulting file handled through an argument, so it is possible to have a separate file for each sub-project

- tmake/lib/win32-g++/generic.t
- tmake/lib/win32-mingw/generic.t
  The destination path was added twice, in case of a depth of more than 1 level (doxmlparser) this lead to problems

- winbuild/Config.rules
- winbuild/Gen_head.rules
- winbuild/Languages.rules
- winbuild/Lex.rules
- winbuild/Settings.rules
- winbuild/Version.rules
  correcting some path of generated files

- winbuild/Doxygen.sln
  Build order dependency could be dropped  as the version.cpp file is now a generated file for doxygen and doxywizard

- winbuild/Doxygen.vcproj
- winbuild/Doxywizard.vcproj
  Corrected paths to the new structure. Added unistd as an external generated file

- winbuild/unistd.h
  File is now generated

- winbuild/Unistd.rules
- winbuild/unistd.py
  Generated unistd for doxygen and doxywizard in a consistent way.

- winbuild/doxyindexer.vcproj
- winbuild/doxysearch.vcproj
- winbuild/qtools.vcproj
  Corrected paths to the new structure.

- winbuild/runbison.bat
- winbuild/version.bat
  Not used anymore everything handled through rules.