Update java code with doxygen tags, add menu files. (#1972)

* Update java code with doxygen tags, add menu files.

* Add -Xdoclint:none to autotools javadoc command

* Committing clang-format changes

* Add fortran RM list descriptions

* delete empty file

* doc tag location changes

* Spelling corrections

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

config/cmake/UseJava.cmake

@@ -1448,6 +1448,7 @@ function(create_javadoc _target)
 
     add_custom_target(${_target}_javadoc ALL
         COMMAND ${Java_JAVADOC_EXECUTABLE}
+                -Xdoclint:none
                 ${_javadoc_options}
                 ${_javadoc_files}
                 ${_javadoc_packages}