Isabelle_System.mkdirs with explicit error checking (in accordance to ML version), e.g. relevant with read-only DMG file-system on Mac OS X;

include /isabelle/rebaseall in autorebaseall, which is run after installation of further packages; patch cygwin in makedist_bundles instead of makedist_cygwin, to avoid frequent repackaging of the same;

do not register quasi-components, notably cygwin;