Improved logger, added a debug timer, other small stuff, and wrote more user guide

docs/Doxyfile

@@ -169,7 +169,7 @@ HTML_HEADER            = header.html
 HTML_FOOTER            = footer.html
 HTML_STYLESHEET        =
 HTML_EXTRA_STYLESHEET  = theme.css
-HTML_EXTRA_FILES       = favicon.png
+HTML_EXTRA_FILES       = images/favicon.png
 HTML_COLORSTYLE_HUE    = 30
 HTML_COLORSTYLE_SAT    = 100
 HTML_COLORSTYLE_GAMMA  = 80
@@ -199,7 +199,7 @@ QHP_SECT_FILTER_ATTRS  =
 QHG_LOCATION           =
 GENERATE_ECLIPSEHELP   = NO
 ECLIPSE_DOC_ID         = org.doxygen.Project
-DISABLE_INDEX          = NO
+DISABLE_INDEX          = YES
 GENERATE_TREEVIEW      = YES
 FULL_SIDEBAR           = NO
 ENUM_VALUES_PER_LINE   = 4