Mostly fixing and standardising documentation.

Doxyfile

@@ -135,7 +135,7 @@ ABBREVIATE_BRIEF       = "The $name class" \
 # description.
 # The default value is: NO.
 
-ALWAYS_DETAILED_SEC    = NO
+ALWAYS_DETAILED_SEC    = YES
 
 # If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all
 # inherited members of a class in the documentation of that class as if those
@@ -162,7 +162,7 @@ FULL_PATH_NAMES        = YES
 # will be relative from the directory where doxygen is started.
 # This tag requires that the tag FULL_PATH_NAMES is set to YES.
 
-STRIP_FROM_PATH        =
+STRIP_FROM_PATH        = src/
 
 # The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of the
 # path mentioned in the documentation of a class, which tells the reader which
@@ -187,7 +187,7 @@ SHORT_NAMES            = NO
 # description.)
 # The default value is: NO.
 
-JAVADOC_AUTOBRIEF      = NO
+JAVADOC_AUTOBRIEF      = YES
 
 # If the QT_AUTOBRIEF tag is set to YES then doxygen will interpret the first
 # line (until the first dot) of a Qt-style comment as the brief description. If
@@ -397,7 +397,7 @@ INLINE_GROUPED_CLASSES = NO
 # Man pages) or section (for LaTeX and RTF).
 # The default value is: NO.
 
-INLINE_SIMPLE_STRUCTS  = NO
+INLINE_SIMPLE_STRUCTS  = YES
 
 # When TYPEDEF_HIDES_STRUCT tag is enabled, a typedef of a struct, union, or
 # enum is documented as struct, union, or enum with the name of the typedef. So
@@ -578,7 +578,7 @@ SORT_MEMBER_DOCS       = YES
 # this will also influence the order of the classes in the class list.
 # The default value is: NO.
 
-SORT_BRIEF_DOCS        = NO
+SORT_BRIEF_DOCS        = YES
 
 # If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the
 # (brief and detailed) documentation of class members so that constructors and
@@ -790,7 +790,7 @@ WARN_LOGFILE           = doxy.log
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = src src/arith src/memory src/ops
+INPUT                  = src
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
@@ -864,7 +864,7 @@ FILE_PATTERNS          = *.c \
 # be searched for input files as well.
 # The default value is: NO.
 
-RECURSIVE              = NO
+RECURSIVE              = YES
 
 # The EXCLUDE tag can be used to specify files and/or directories that should be
 # excluded from the INPUT source files. This way you can easily exclude a