* template and function arguments
* innernamespaces
* put sqlite3_stmt and the coresponding query in
  a struct
* use has(Multi|One)LineInitializer instead of hardcoded value
  when extracting references from initializers
* sqlite3_clear_bindings in step()
* getRow in step() should use different sqlite3_ functions
  depending on wether is doing 'INSERT' or 'SELECT'

includes table uses only file IDs
Signed-off-by: Adrian Negreanu <adrian.m.negreanu@intel.com>

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.

Bug 723299 - Last line of code block lost if it is only one character and there is no text afterward

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.

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

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.

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>

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

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.

The following code should produce two groups, each containing one page, within the same documentation scope,
currently it nests these groups and pages, resulting in incorrect documentation.

--! \defgroup group1 Group 1
--! \{
--!   @brief Group 1
--! \}

--! \ingroup group1
--! \{
--! \page group1_page1 Page 1
--! \verbatim
--!  Some Page 1 text
--! \endverbatim
--! \}

--! \defgroup group2 Group 2
--! \{
--!   @brief Group 2
--! \}

--! \ingroup group2
--! \{
--! \page group2_page1 Page 1
--! \verbatim
--!  Some Page 1 text
--! \endverbatim
--! \}

Similar C code to demonstrate the correct output.

//! \defgroup group1 Group 1
//! \{
//!   @brief Group 1
//! \}

//! \ingroup group1
//! \{
//! \page group1_page1 Page 1
//! \verbatim
//!  Some Page 1 text
//! \endverbatim
//! \}

//! \defgroup group2 Group 2
//! \{
//!   @brief Group 2
//! \}

//! \ingroup group2
//! \{
//! \page group2_page1 Page 1
//! \verbatim
//!  Some Page 1 text
//! \endverbatim
//! \}

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)

The utf-8 code for eta was identical to the code for theta and the code for Prime was identical to the one for prime

* call sqlite3_clear_bindings when step fails
* more miss-placed returns
Signed-off-by: Adrian Negreanu <adrian.m.negreanu@intel.com>

Corrected some spelling errors and added / correceted some references