Doxygen Doxyfile Changes I Usually Do (To the Default Generated File)

RECURSIVE = YES
EXTRACT_ALL = YES
REFERENCES_RELATION    = YES
REFERENCED_BY_RELATION = YES

the following for browsing through sources:
SOURCE_BROWSER = YES
INLINE_SOURCES = YES
EXTRACT_PRIVATE = YES
EXTRACT_STATIC = YES
EXTRACT_LOCAL_CLASSES = YES

for collaboration diagrams:
HAVE_DOT =YES

Excluding Multiple Directories using Doxygen EXCLUDE tag

After a lot of search I found at http://developer.kde.org/documentation/library/howto.php how one can specify multiple excluded sub-directories in the following format:

EXCLUDE = {directory 1} {directory 2} ...

Doxygen is such a nifty tool. The pleasure would have been additional if the config files contained very simple format examples.

Default Doxyfile for Code Understanding

The most often use-case of doxygen for me is to quickly understand the source code. Several of the configurations within the default-generated doxyfile are different from the way you would like it to be to generate detailed information for understanding the code. Below I paste the diff that can be used to patch the default generated doxyfile to configure it for code understanding. The config below assumes we have installed the "dot" tool (installing dot is a good idea anyway as it is a nifty graph display tool).

28c28
< project_name =" ---"> PROJECT_NAME = project_name
300c300
< extract_all =" NO"> EXTRACT_ALL = YES
305c305
< extract_private =" NO"> EXTRACT_PRIVATE = YES
310c310
< extract_static =" NO"> EXTRACT_STATIC = YES
473c473
< show_directories =" NO"> SHOW_DIRECTORIES = YES
590c590
< recursive =" NO"> RECURSIVE = YES
683c683
< source_browser =" NO"> SOURCE_BROWSER = YES
688c688
< inline_sources =" NO"> INLINE_SOURCES = YES
700c700
< referenced_by_relation =" NO"> REFERENCED_BY_RELATION = YES
706c706
< references_relation =" NO"> REFERENCES_RELATION = YES
738c738
< alphabetical_index =" NO"> ALPHABETICAL_INDEX = YES
977c977
< generate_latex =" YES"> GENERATE_LATEX = NO
1342c1342
< have_dot =" NO"> HAVE_DOT = YES
1390c1390
< uml_look =" NO"> UML_LOOK = YES
1482c1482
< dot_transparent =" NO"> DOT_TRANSPARENT = YES