Update paths for generating documentation.

Documentation/Doxyfile.in

@@ -775,19 +775,7 @@ WARN_LOGFILE           =
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = ${CMAKE_SOURCE_DIR}/Applications \
-                         ${CMAKE_SOURCE_DIR}/AssemblerLib \
-                         ${CMAKE_SOURCE_DIR}/BaseLib \
-                         ${CMAKE_SOURCE_DIR}/Documentation \
-                         ${CMAKE_SOURCE_DIR}/FileIO \
-                         ${CMAKE_SOURCE_DIR}/GeoLib \
-                         ${CMAKE_SOURCE_DIR}/MathLib \
-                         ${CMAKE_SOURCE_DIR}/MeshGeoToolsLib \
-                         ${CMAKE_SOURCE_DIR}/MeshLib \
-                         ${CMAKE_SOURCE_DIR}/NumLib \
-                         ${CMAKE_SOURCE_DIR}/ProcessLib \
-                         ${CMAKE_SOURCE_DIR}/README.md \
-                         ${CMAKE_SOURCE_DIR}/SimpleTests
+INPUT                  = ${CMAKE_SOURCE_DIR}/
 
 # 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
@@ -830,7 +818,9 @@ RECURSIVE              = YES
 # Note that relative paths are relative to the directory from which doxygen is
 # run.
 
-EXCLUDE                = ${CMAKE_SOURCE_DIR}/ThirdParty
+EXCLUDE                = ${CMAKE_SOURCE_DIR}/ThirdParty \
+                         ${CMAKE_SOURCE_DIR}/scripts \
+                         ${CMAKE_SOURCE_DIR}/Tests
 
 # 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