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.

detect python2 as Python 2 binary

On some distributions like Arch Linux
"python" is Python 3 and "python2" is Python version 2.

We now try "python2" first and use it if available.

Add extra (documenation) directories to ignore pattern

Better message in case doxygen -u is used

Error message is given for make distclean as generated_src is a directory

In case of obsolete or not configured entries in the Doxyfile and the option -u is used a message like:
  Warning: Tag `XML_DTD' at line 1821 of file Doxyfile has become obsolete.
  To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
appears, but the item is removed from the Doxyfile.
This patch updates the message (and improves layout) to:
  Warning: Tag `XML_DTD' at line 1821 of file `Doxyfile' has become obsolete.
                  This tag has been removed.

Add docbook directory to be removed as well

Add extra (documenattion) directories to ignore pattern

generated_src is a directory and should be removed with the -rf flag.
Similar for other directories like bin, objects, lib, html latex, objects.
Directories man, rtf, perlmod, xml have been added for convenience (when testing with other documentation formats)

Items XML_SCHEMA and XML_DTD declared obsolete

The items XML_SCHEMA and XML_DTD are not used and there is no plan for using them, so declared obsolete.

Merge branch 'wip/fix-link-id-on-last-line' of https://github.com/agateau/doxygen into agateau-wip/fix-link-id-on-last-line

Conflicts:
	testing/055/md_055_markdown.xml
	testing/055_markdown.md

In the chm-doxygen manual we see that for:
- the command \& the & is missing
- commands containing a " all text is missing after this "
These are known limitations of the chm format (see e.g.
http://www.helpware.net/htmlhelp/hhwreadme.htm)

Ids created from the last line were not lower-cased, leading to the link
not being recognized.

MAN_SUBDIR parameter

sqlite3 fixes

Add line numbers in case comment is not closed properly.

Enabling possibility to have { and } in (latex) index items

This verifies the 'memberdef' table against the generated XMLs.
It accomplishes this by executing a sql query, constructed by iterating
through the children and attributes of the memberdef XML element.

The information translated from xml to sql, is then removed from the DOM,
and the unprocessed bits are printed as warning messages.

usage:
    testing/testsqlite3.py -d /.../doxygen_sqlite3.db -x /.../xml/test__x11_8cpp.xml

output:
WARNING: 'location' has unprocessed attr 'bodyend'
WARNING: 'memberdef' has unprocessed child elem 'briefdescription'
WARNING: 'memberdef' has unprocessed child elem 'detaileddescription'
WARNING: 'memberdef' has unprocessed child elem 'inbodydescription'
WARNING: 'memberdef' has unprocessed child elem 'location'
WARNING: 'memberdef' has unprocessed attr 'kind'
WARNING: 'memberdef' has unprocessed attr 'prot'
WARNING: 'memberdef' has unprocessed attr 'static'
WARNING: 'memberdef' has unprocessed attr 'id'

In table basecompoundref, use SQLITE_TRANSIENT for
base, derived, refid

memberdef table changes:
* rename bstart to bodystart
* rename id_bfile to id_bodyfile
* add bodyend
* add {brief,detailed,inbody}description
Signed-off-by: Adrian Negreanu <adrian.m.negreanu@intel.com>

sqlite3: fedora has libsqlite3.so in /usr/lib64

Signed-off-by: Adrian Negreanu <groleo@gmail.com>

This bug fix is an extension to the bug fix:  Add warning when encountering a nested comment start (/*) without matching end (*/).
It is quite hard to find the place in the source file where the problem occurs. This bug fix helps to locate part of the problems, it is not perfect it only gives the starting comment tags that give a problem (other problems also occur e.g. when // is followed by */).

Bug 722759 - Documentation for derived classes no longer has an "Additional Inherited Members" section after upgrading Doxygen from 1.8.3.1 to 1.8.6

Incorrect handling dependencies

The handling of a number of dependencies was incorrect, it was stated that the i(source) cpp file depended on the (included) h file, this should be that the resulting (object) o file depends on the cpp and the h file. See e.g. the layout.cpp dependency
Some dependencies used ../generated_src/doxygen it is better to use the definition GENERATED_SRC

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.