Doxygen: Better path handling.

This change tells doxygen to include all files not explicitly
excluded, and to document paths along with filenames.

Doxyfile.in

@@ -161,7 +161,7 @@ INLINE_INHERITED_MEMB  = NO
 # shortest path that makes the file name unique will be used
 # The default value is: YES.
 
-FULL_PATH_NAMES        = NO
+FULL_PATH_NAMES        = YES
 
 # The STRIP_FROM_PATH tag can be used to strip a user-defined part of the path.
 # Stripping is only done if one of the specified strings matches the left-hand
@@ -173,7 +173,7 @@ FULL_PATH_NAMES        = NO
 # 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        = @top_srcdir@/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
@@ -816,10 +816,7 @@ WARN_LOGFILE           =
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = @top_srcdir@/src/lib \
-                         @top_srcdir@/src/core \
-                         @top_srcdir@/src/feature \
-                         @top_srcdir@/src/app
+INPUT                  = @top_srcdir@/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
@@ -861,7 +858,9 @@ RECURSIVE              = YES
 # Note that relative paths are relative to the directory from which doxygen is
 # run.
 
-EXCLUDE                =
+EXCLUDE                = @top_srcdir@/src/ext \
+                         @top_srcdir@/src/trunnel \
+                         @top_srcdir@/src/test
 
 # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
 # directories that are symbolic links (a Unix file system feature) are excluded