Changes

Summary

1. merged
2. renamed ISABELLE_BUILD_JAVA_OPTIONS to ISABELLE_TOOL_JAVA_OPTIONS;
3. clarified SML name space: no access to structure PolyML;
4. prefer internal tool;
5. isabelle update_cartouches -c -t;
6. prefer internal tool;
7. prefer internal tool -- assuming that ISABELLE_TMP_PREFIX is created properly by Isabelle_System.isabelle_tmp_prefix;
8. prefer internal tool;
9. prefer internal tool;
10. prefer internal tool;
11. prefer internal tool;
12. support for internal tools;
13. clarified Isabelle tool wrapper: bash, Scala, no perl, no ML;
14. clarified usage;