On windows citelist.doc remains

On windows the file citelist.doc is not removed as it is not closed. This patch closes the file.

sqlite3 updates

+  -I <I>    Get the includers of <I>
+  -i <I>    Get the includees of <I>
+  -M <C>    Get all members of class <C>
+  -B <C>    Get the base classes of class <C>
+  -S <C>    Get the sub classes of class <C>
Signed-off-by: Adrian Negreanu <adrian.m.negreanu@intel.com>

* 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>

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