Changes

Summary

1. merged
2. clarified init_session_base / finish_session_base: retain some information for plain "isabelle process", without rechecking dependencies as in "isabelle console";
3. clarified directories;
4. tuned signature (again);
5. proper bootstrap base for building Pure;
6. tuned according to Scala version;
7. more global theories;
8. tuned;
9. clarified loaded_theories: map to qualified theory name; proper theory_name for PIDE editors;
10. global session_base for PIDE interaction;
11. more explicit jEdit file operations; less redundant JEdit_Resources.node_name();
12. early check and normalization of session directory, e.g. relevant for path information passed to ML process, which may have a different CWD;
13. tuned;