directed graphs, a five minute discussion with Dave has led to a
revised specification for handling multiple files. This should be
easier to implement and more efficient. Directed graphs are
no longer required.
Removed isabelle-settings defcustom, renamed to isabelle-.
Renamed some customization variables isabelle-* for nice
display in menus. Removed proof-assistant setting.
Removed proof-global-p and isa-global-p. Renamed isa-thy-mode
to thy-mode.