This patch describes an alternative way to get rules / debug information from flex files

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.

Made documentation for custom commands more consistent and remove not required backslashes

Some superfluous backslashes were found in the documentation (1.8.6 manual page 52, diagrams section)

In doxygen a limited number of HTML4 special character entities are recognized, with this patch the full list of HTML4 special character entities (see http://www.w3.org/TR/html4/sgml/entities.html) is supported (as far as they can be represented in the output format).

- doxygen_manual.tex
- latexgen.cpp
  Added wasysym package to support per thousand sign (perthousand command from textcomp didn't work properly)
  Added option for textcomp package so currency symbol would work properly

- htmlcmds.doc
  Adjusted documentation, listing all entities

- compound.xsd
- xmlgen.cpp
  Removed in xsd file all references for special HTML4 character entities and placed placeholder so doxygen (in xmlgen.cpp)can automatically add the right element names.

- util.cpp
- util.h
  Define all entities with their representation for all output formats.
  Define access routines to the different representations
  Mapping (for recognition of the entities) based on running through the list of available entities, after validation of the order of the entities. A few entities contain now besides letters also numbers at the end.

- docparser.h
  Define symbols for all entities as well as a helper struct and enum. The member m_letter is not used anymore and thus removed.
  All existing symbols were renamed so no confusion (i.e. errors when forgetting to rename some symbols) can occur.
  Obsolete references to letter removed, all letters with accents etc. are explicitly defined and not through the generic accent name plus an extra letter.

- docparser.cpp
  Adjust used symbols to their new names.
  Remove references to letter (as used for accents etc.)
  Replace list of explicitly supported entities with call to symbol code access routine.

- docbookvisitor.cpp
- htmldocvisitor.cpp
- latexdocvisitor.cpp
- mandocvisitor.cpp
- perlmodgen.cpp
- printdocvisitor.h
- rtfdocvisitor.cpp
- textdocvisitor.cpp
- xmldocvisitor.cpp
  Replace list of explicitly supported entities with call to access routine and use returned value to output.

In the doxygen manual the index items for \{ and \} were missing due to the missing support for the usage of { and } in parts of the code.
This patch fixes this problem by introducing 2 new latex commands. See also http://tex.stackexchange.com/questions/153291/index-unmatched-braces-in-latex
Further improvements in the index are:
- consistency in different places
- correction of index for \::
- placing \~ on a more logical place (together with other special characters, ~ is in the ASCII table after a-z whilst other characters are before this range)

Adjusted documentation so that -- in \c and <code> are shown as -- by placing the parts in ` (backtick)

Corrected some spelling errors and added / correceted some references

Adjusted documentation and in case the title is the empty string in a DocXRefItem the visitPre and visitPost do nothing.

Update the documentation in respect to the version of flex and bison that can be used.

Patch regarding generating the rules file for the windows build regarding languages, some inconsistencies in the (windows) build system, corrections to some spelling.

- maintainers.txt
Spelling correction

- config.xml
Added missing languages
Extended some descriptions

- htmlhelp.cpp
Added missing languages
Spelling corrections

- language.cpp
Corrected call in respect to Serbian-Cyrillic

- translator_br.h
Spelling correction

- translator_fa.h
Corrected (not used) define in respect to LeftToRight

- translator_mk.h
Spelling correction

- translator_sc.h
Corrected in respect to consistency for Serbian-Cyrillic

- Doxygen.sln
Added project dependency as otherwise there might be a problem with the generation of version.cpp

- Doxygen.vcproj
Added rules for selecting languages to be used during translation
Corrected some incorrect references / directories
Corrected names of generated files / directories so they won't overwrite / conflict (especially during parallel builds)
Corrected name of genhead <-> gen_head (consistency with rules file)

- Doxywizard.vcproj
Corrected some incorrect references / directories
Corrected names of generated files / directories so they won't overwrite / conflict (especially during parallel builds)
Note place of resulting executable has hanged (more consistent now)

- Settings.rules
Corrected place where configure file can be found

- Version.rules
Corrected place where configure file can be found

- doxyindexer.vcproj
Corrected some incorrect references / directories
Corrected names of generated files / directories so they won't overwrite / conflict (especially during parallel builds)

- doxysearch.vcproj
Corrected some incorrect references / directories
Corrected names of generated files / directories so they won't overwrite / conflict (especially during parallel builds)

- iconv.vcproj
Corrected some incorrect references / directories
Corrected names of generated files / directories so they won't overwrite / conflict (especially during parallel builds)

- qtools.vcproj
Corrected some incorrect references / directories
Corrected names of generated files / directories so they won't overwrite / conflict (especially during parallel builds)

- lang_cfg.py
Script to generate the file lang_cfg.h based on the specified languages in the windows GUI or in the configure script.

- languages.py
Script to generate languages pane in the windows GUI
This file has to be called outside visual studio as it generates the rules for the Languages pane in the GUI (command on src directory python languages.py > ..\winbuild\Languages.rules)

- Languages.rules
Result file from language.py (old file was completely wrong and not used)
This file has to be generated outside visual studio as it contains the rules for the Languages pane in the GUI

- configure
Use lang_cfg.py script (consistency) instead of (internal) perl script.

This patch contains changes regarding the build system so that the *nix and Windows systems use the same information (consistency). Some use names routine names have been changed (from .l files with -P option) to reflect the file name that generated the routines, this makes it easier to create a general procedure.
A number of include / header files are files are generated from different file types (html, xml, js), due some limitations of the windows build system the generated file names had to be changed (the extension in the windows build system is only available including the '.' so e.g. the file jquery_fx.js generates now jquery_fx.js.h instead of jquery_fx_js.h)
In the windows version the creation of .cpp files from .l files has been adjusted to correct for the YY_BUF_SIZE problems.
Furthermore on windows (and also used on *nix) some commends have been replaced with python scripts so that on windows only python is need (besides flex and and bison). On *nix also perl is required for the generation using tmake.

Below a short description of the changes will be given and grouped.

Changed files
=============
- .gitignore
added some directories and file

- Doxyfile
corrected for changed file names

- Makefile.in
added realclean and some other changes (ignore error) and the moment when the Makefile is deleted (as last file).
Added entries for doxyapp and doxmlparser

Added realclean for the following files (consistency):
======================================================
- Makefile.win_make.in
- Makefile.win_nmake.in
- addon/doxmlparser/examples/metrics/Makefile.in
- addon/doxmlparser/src/Makefile.in
- addon/doxmlparser/test/Makefile.in
- addon/doxyapp/Makefile.in
- addon/doxysearch/Makefile.in
- libmd5/Makefile.in
- qtools/Makefile.in

- addon/doxyapp/doxyapp.pro.in
removed double occurence of -L../../lib

- addon/doxysearch/doxysearch.pro.in
no visible change just spacing?

- addon/doxywizard/Makefile.in
added realclean
corrected call to qmake (to get it from the right place, it is not necessarily in the path)
made some macros known in the called process

- addon/doxywizard/configdoc.cpp
automatically generated, can be removed

- addon/doxywizard/doxywizard.pro.in
corrected dependencies
corrected call to python (to get it from the right place, it is not necessarily in the path)
new items to generate version.cpp and config_doxyw.cpp

- configure
added configuration definition possibility for python
added possibility to build doxmlparser
automatically generate the lang_cfg.h file based on the available languages (translator_??.h) and not on a fixed list. This step still has to be added to the windows build process.

- doc/Makefile.in
corrected call to python (to get it from the right place, it is not necessarily in the path)

- doc/config.doc
small correction

- doc/install.doc
added python as a requirement
changed CVS to GitHub

- doc/language.doc
automatically generated file, based on other changes.

- doc/language.tpl
made XX and xx more consistent
changed description of the procedure based on changes already made configure.

- src/Makefile.in
adjusted used file names in distclean
Solved PERL usage consistent with LEX / YACC (with %%PERL%%)
automatically add translator_??>h to HEADERS
same spacing

Adjusted in the following file the names of some include files:
===============================================================
- src/cite.cpp
- src/docbookgen.cpp
- src/ftvhelp.cpp
- src/htmlgen.cpp
- src/layout.cpp
- src/searchindex.cpp
- src/xmlgen.cpp

Adjusted in the following files some routine names (..YY..) to be consistent with the file names:
=================================================================================================
- src/commentscan.l
- src/constexp.h
- src/constexp.l
- src/constexp.y
- src/fortrancode.l
- src/fortranscanner.l
- src/pyscanner.l
- src/pre.l
- src/scanner.l
- src/tclscanner.l
- src/vhdlparser.y
- src/vhdlscanner.l

- src/config.xml
small textual correction

- src/configoptions.cpp
generated output file, can be removed

- src/lang_cfg.h
Automatically generated file with selected languages (*nix). On windows a procedure has to be defined.

- src/libdoxycfg.t.in
corrected call to python (to get it from the right place, it is not necessarily in the path)

- src/libdoxygen.pro.in
adjusted include file names
removed translator_??.h files, they are added automatically
changed file name ce_lex.cpp -> constexp.cpp (generated file)

- src/libdoxygen.t.in
made LEX calls used the file name for the -P option
changed INCREASEBUF script to a python script
changed teh geneartion of some include file, now by means of a pythons script. Names of the generated include file had to be changed as well.
added possibility to generate version.cpp here as well.

Added HEADERS to dependency so non existing but later generated include files are recognized as well:
=====================================================================================================
- tmake/lib/unix/generic.t
- tmake/lib/win32-borland/generic.t
- tmake/lib/win32-g++/generic.t
- tmake/lib/win32-mingw/generic.t
- tmake/lib/win32-msvc/generic.t
- tmake/lib/win32-symantec/generic.t
- tmake/lib/win32-visage/generic.t
- tmake/lib/win32-watcom/generic.t

- winbuild/Doxygen.vcproj
made consistent wit *nix version.
Generating all possible files
removed unused /empty parts
setting for the Lex.rules and other rules files some default values

- winbuild/Doxywizard.vcproj
made consistent wit *nix version.
Generating all possible files
removed unused /empty parts
removed system dependent paths (C:\... etc) replaced then with external environment variables

- winbuild/Lex.rules
adjusted file to comply with new requirements, only user variable is -d. -i is set to read only (value can be changed  in doxygen.vcproj). Handling of other arguments is all default.
generation including increasebuffer possibility

- winbuild/doxyindexer.vcproj
corrected path

- winbuild/doxysearch.vcproj
removed system dependent paths (C:\... etc) replaced then with external environment variables

- winbuild/qtools.vcproj
corrected type, wrong used directory

The following files are automatically generated (with slightly other names like index.xsd.h etc.):
==================================================================================================
- src/index_xsd.h
- src/doxygen_bst.h
- src/dynsections_js.h
- src/extsearch_js.h
- src/footer_html.h
- src/header_html.h
- src/jquery_fx_js.h
- src/jquery_p1_js.h
- src/jquery_p2_js.h
- src/jquery_p3_js.h
- src/jquery_pt_js.h
- src/jquery_ui_js.h
- src/navtree_css.h
- src/navtree_js.h
- src/resize_js.h
- src/search_css.h
- src/search_functions_php.h
- src/search_js.h
- src/search_opensearch_php.h
- src/svgpan_js.h
the following files are generated with different names:
- src/bib2xhtml.h
becomes
- src/bib2xhtml.pl/h

- src/layout_default.h
becomes
- src/layout_default.xml.h

The file:
=========
- addon/doxywizard/config.l
is replaced by:
- addon/doxywizard/config_doxyw.l
so there are in the system not 2 different config.l files. Renamed some routines from configYY -> config_doxywYY...

New files:
==========
- src/increasebuffer.py
increase YY_BUF_SIZE and YY_READ_BUF_SIZE from 16k / 8k to 256k.

- src/settings.py
create settings.h file

- src/to_c_cmd.py
create include files from different files (html, xml, js) so they can be included in the code as defaults

- src/version.py
create version.cpp file based on the configure file

- winbuild/Config.rules
rules file to convert the config.xml file into configoptions.cpp (doxygen) or configdoc.cpp (doxywizard). Seen the differences 2 rules are created within this file.

- winbuild/Gen_head.rules
rules files to generate include files from different files using to_c_cmd.py

- winbuild/Settings.rules
rules file for generating the settings.h file. It is possible to select to use CLANG and SqlLite3

- winbuild/Version.rules
rules file to be able to start version.py

The files:
==========
- version.bat
- runbison.bat
- increasebuffer.pl
are not used anymore.

I've only added the files as indicated, I didn't remove the files from the repository.

Made documentation more inline with other parts of the documentation (regarding the way e.g. filenames are presented)
Corrected some spelling errors
Corrected the warning in the language.doc by placing ta reference to the files from which language.doc is generated
Corrected the color for the languages that are still v1.4.6 (language name now also red  in stead of a pink background, was confusing with languages that were 1.5 / 1.6 compatible)

The "almost up-to-date" category of the language translator classes
introduced. Together with the background colouring (green, yellow, pink,
red), it is mostly the psychological move towards language maintainers :)