ROOTS

more uniform Isabelle_System.mkdirs in ML/Scala;
avoid odd permission problems on Windows (e.g. Desktop) by using "mkdirs" from Cygwin;

src/Pure
src/FOL
src/HOL
src/ZF
src/CCL
src/CTT
src/Cube
src/FOLP
src/LCF
src/Sequents
src/Doc
src/Tools