clarified signature according to Scala version;

clarified Isabelle tool wrapper: bash, Scala, no perl, no ML;

File.bash_string operations in ML as in Scala -- exclusively for GNU bash, not perl and not user output;
clarified treatment of whitespace in some bash scripts;

clarified File.standard_path vs. File.platform_path (like Isabelle/Scala operations);
avoid patching of SML basis library;

more portable mkdirs via perl, e.g. relevant for Windows UNC paths (network shares);

avoid redundant shell process;

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

removed unused/non-portable with_tmp_fifo;

clarified copy_file: allow to rename base name, e.g. relevant for 'display_drafts';

explicit 'document_files' in session ROOT specifications;
clarified Isabelle_System.copy_file(_base): preserve file-attributes and local directory hierarchy;

tuned comments (see Scala version);

removed unused/non-portable bash_output_fifo;

redirect bash stderr to Isabelle warning as appropriate -- avoid raw process error output which may either get ignored or overload PIDE syslog in extreme cases;

more uniform / portable representation of the idea of "copy_dir" (NB: cp -f dereferences symlinks on GNU/Linux, but does not on old-school Unixen including BSD/Mac OS X);

tuned comment;

bash_output_fifo blocks on Cygwin 1.7.x;

clarified bash_output_fifo;

moved bash operations to Isabelle_System (cf. Scala version);

access to process output stream via auxiliary fifo;

prefer Isabelle path algebra;

Isabelle_System.create_tmp_path/with_tmp_file: optional extension;
thread-safe versions of Present.display_graph, Present.isabelle_browser, Present.drafts -- using Isabelle_System.with_tmp_dir;

Path.print is the official way to show file-system paths to users -- note that Path.implode often indicates violation of the abstract datatype;

make SML/NJ and Poly/ML agree on the type of "before";

slightly more standard Isabelle_System.with_tmp_file/with_tmp_dir (cf. Scala version);
more robust rm_tree -- somewhat dangerous and not exported;
tuned;

more permissive Isabelle_System.mkdir;
exported File.is_dir (weak test);

more basic Isabelle_System.mkdir;

more explicit Isabelle_System operations;