tuned -- use existing operation;

clarified signature: flexible base_dir;

more accurate isabelle_id: parent directory is not necessarily at tip;

more uniform id;

tuned imports;

more robust: avoid global change of LD_LIBRARY_PATH (e.g. relevant for subprocesses);

tuned;

more robust update of generated directory;
tuned;

tuned;

more robust: tmp files might get deleted concurrently in ML vs. Scala process;

tuned;

insist in proper GNU tar, to avoid subtle semantic differences;

clarified modules;

prefer standard_path for bash arg;

clarified modules;

expand relatively to given environment, notably remote HOME;

prefer Isabelle standard Path;

clarified file operations;

tuned signature;
copy_dir using *this* Isabelle_System: note that File.bash_path is already expanded, but no variables are used here;

support remote repositories via ssh command execution;
tuned;

explicit indication of Admin tools;

--HG--
rename : src/Pure/Tools/build_doc.scala => src/Pure/Admin/build_doc.scala
rename : src/Pure/Tools/build_stats.scala => src/Pure/Admin/build_stats.scala
rename : src/Pure/Tools/check_sources.scala => src/Pure/Admin/check_sources.scala
rename : src/Pure/Tools/remote_dmg.scala => src/Pure/Admin/remote_dmg.scala

enforce short name, notably on Mac OS X;

tuned signature;

basic setup for Admin/build_history -- outside of Isabelle environment;

tuned;

find heaps uniformly via Sessions.Store;
tuned;

tuned;

tuned signature;

prefer Scala over bash function;

tuned;

clarified env;

unused;

more uniform signature for various process invocations;
env refers to full environment, not the update;

more thorough cleanup -- in Scala;

isabelle.Build uses ML_Process directly;
isabelle_process is for batch mode only;
removed unused feeder (already part of "isabelle console");

Bash.process always uses a closed script instead of an open argument list, for extra robustness on Windows, where quoting is not well-defined;
more robust File.bash_escape;
more robust treatment of ML_OPTIONS;
clarified prover args (again);

clarified modules;

more informative Build.build_results;
tuned signature;

more informative Process_Result;
tuned;

clarified modules;

more direct invocation of ISABELLE_BASH_PROCESS on Windows;

tuned signature;

tuned signature -- more like ML version;

clarified bash process -- similar to ML version;

tuned signature;

more direct task future implementation, with proper cancel operation;
more uniform Future.thread;

clarified modules;

--HG--
rename : src/Pure/Concurrent/simple_thread.ML => src/Pure/Concurrent/standard_thread.ML
rename : src/Pure/Concurrent/simple_thread.scala => src/Pure/Concurrent/standard_thread.scala

proper Cygwin.init (amending e00e1bf23d03);

clarified ISABELLE_ROOT (platform path) vs. ISABELLE_HOME (standard path);

uniform treatment of bootstrap directories;
Isabelle_System.init() includes Cygwin.init(), e.g. for situations without isabelle.Main;
tuned;

clarified Isabelle_System.init;
clarified GUI.init_laf;
clarified modules;
tuned signature;

tuned;

clarified kill on Windows: just one executable;

clarified modules, like ML version;

clarified modules, like ML version;

tuned signature, according to ML version;

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;

misc tuning, based on warnings by IntelliJ IDEA;

tuned message, in accordance to ML side;

prefer original TEMP from Windows, e.g. relevant for Isabelle distribution within read-only directory (due to its bundled Cygwin and /tmp inside of it);

sane environment defaults for Mac OS X, based on former App1/script -- e.g. relevant for MacTeX PATH;

expose interrupts more like ML version, but not in managed bash processes of Build;

more robust process kill -- postpone interrupts on current thread;

basic support for Mercurial command line tools;

more abstract Exn.Interrupt and POSIX return code;

avoid accidental use of scala.language.reflectiveCalls;

avoid octal escape literals -- deprecated in scala-2.11.0;

tuned signature -- separate module Word;

more native rm_tree, using Java 7 facilities;

support for URL as file name, similar to treatment in jEdit.java;

more standard Isabelle_System.tmp_file and tmp_dir operations, in accordance to ML version;

tuned signature;

tuned imports;

prefer concrete list append;

avoid hardwired /bin/bash (like canonical Isabelle shell scripts);

more direct Isabelle_System.pdf_viewer;
generic Isabelle_System.open, e.g. for URLs;

more robust and portable invocation of kill as bash builtin, instead of external executable -- NB: /bin/kill on Mac OS X Mountain Lion chokes on Linux workaround from 3610ae73cfdb;

tuned whitespace;

more robust System.getProperty with default;

Scala version of init.bat;

--HG--
rename : src/Pure/System/cygwin.scala => src/Pure/System/cygwin_init.scala

more robust command line -- accomodate /bin/kill on recent Linux (e.g. Xubuntu 13.04):

timeout counts as regular error, with rc = 1 (cf. special Exn.Interrupt vs. regular TimeLimit.TimeOut in Isabelle/ML);

recovered informative progress from 016cb7d8f297;

limit build process output, to avoid bombing Isabelle/Scala process by ill-behaved jobs (e.g. Containers in AFP/9025435b29cf);

cygwin_root as optional argument;
tuned;

separate module "GUI", to keep this out of the way of generic Isabelle_System operations, notably for non-Isabelle/jEdit applications;
tuned signature;

separate module Isabelle_Font, to keep this out of the way of generic Isabelle_System operations, notably for non-Isabelle/jEdit applications;

more robust handling of repeated interrupts while terminating managed process;
NB: InterruptedException should have interrupted status cleared already;

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;

add icon for toplevel windows;

immediate theory progress for build_dialog;
more formal Bash_Result -- accumulate output as lines;

prefer old graph browser in Isabelle/jEdit, which still produces better layout;
clarified print mode "active_graph": allow to switch "browser" vs. "graphview" uniformly;
tuned signature;

support File.read_gzip as well, in accordance to File.write_gzip;
tuned signature;

tuned signature -- eliminated obsolete Standard_System;

tuned signature;

more uniform default logic, using settings, options, args etc.;
clarified build_dialog -C: imitate jEdit logic selection more precisely;

tuned import;

explicit module UTF8;

JavaFX is inactive by default;

load fonts into JavaFX as well;

prefer jEdit file name representation (potentially via VFS);
tuned;

tuned signature;

simplified Path vs. JVM File operations;

tuned;

some actual build function on ML side;
further imitation of "usedir" shell script;

more abstract file system operations in Scala, corresponding to ML version;

more explicit java.io.{File => JFile};

further imitation of "usedir" shell script;
Pure/build observes build_images option, unlike traditional version;
tuned signature;

support for detached Bash_Job with some control operations;

support external processes with explicit environment;

avoid Source.fromFile, which does not necessarily close its input;

prefer sys.env from scala 2.9;

cold-start HOME is user.home, in accordance with Cygwin-Terminal.bat;

more robust handling of PATH vs PATH_JVM -- required for cold start of Cygwin from Windows (e.g. Isabelle.exe);

USER_HOME settings variable points to cross-platform user home directory;

ISABELLE_JDK_HOME settings variable points to JDK with javac and jar (not just JRE);
update for prospective jdk1.7.x component;

prefer sorting from Scala library;

proper platform_file_url for Windows UNC paths (server shares);

proper platform_file_url;

more abstract wrapping of fifos as System_Channel;

reduced verbosity;

simplified Symbol based on lazy Symbol.Interpretation -- reduced odd "functorial style";
tuned implicit build/init messages;

prefer space_explode/split_lines as in Isabelle/ML;

Path.split convenience;

tuned;

quasi-static Isabelle_System -- reduced tendency towards "functorial style";

explicit class Counter;

prefer Isabelle path algebra;

explicit import java.lang.System to prevent odd scope problems;

lazy Isabelle_System.default supports implicit boot;

simplified/generalized ISABELLE_FONTS handling;

suppress Mercurial backup files;
uniform treatment of tool filtering in bash/perl/scala;

tuned mk_fifo;

eliminated Simple_Thread shorthands that can overlap with full version;

more robust Managed_Process.kill: check after sending signal;

more robust lib/scripts/process, with explicit script/no_script mode;
added general Isabelle_System.Managed_Process, with bash_output as application;
tuned;

refined Isabelle_System.bash_output: pass pid via stdout, separate stdout/stderr;

refined ML/Scala bash wrapper, based on more general lib/scripts/process;

--HG--
rename : lib/scripts/bash => lib/scripts/process

more robust Isabelle_System.rm_fifo: avoid external bash invocation, which might not work in JVM shutdown phase (due to Runtime.addShutdownHook);

simplified Isabelle_System.mk_fifo: inlined script, append PPID and PID uniformly;

simplified fifo handling -- rm_fifo always succeeds without ever blocking;
tuned;

Isabelle_System.mk_fifo: more robust enumeration of unique names, based on persisting JVM pid (parent of shell process);

do not buffer fifo streams here -- done in Isabelle_Process;
removed misleading comments -- blocking on open is not reliable on non-standard systems (Cygwin);

uniform raw_dump for input/output fifos on Cygwin;

Isabelle_Process: separate input fifo for commands (still using the old tty protocol);
some partial workarounds for Cygwin;

clarified font_family vs. font_family_default;
install_fonts: refrain from any magic that does not really work on Mac OS, but introduces strange problems on other platforms;

indicate prospective properties;

rendering information and style sheets via settings;
generalized Isabelle_System.try_read;
prefer getenv_strict in most situations;

Isabelle_System: allow explicit isabelle_home argument;

general Isabelle_System.try_read;

more convenient get_font;

more convenient get_font;

explicit getLines(n) ensures platform-independence -- our files follow the POSIX standard, not DOS;

improved ISABELLE_JAVA, based on THIS_JAVA of the actually running JVM;

more precise treatment of UNC server prefix, e.g. //foo;

replaced some deprecated methods;

adapted to Scala 2.8.0 Beta1 -- with notable changes to scala.collection;

modernized perl scripts: prefer standalone executables;
exec bash wrapper script directly -- avoid intermediate process;

--HG--
rename : lib/scripts/system.pl => lib/scripts/bash

renamed system/system_out to bash/bash_output -- to emphasized that this is really GNU bash, not some undefined POSIX sh;

--HG--
rename : src/Pure/ML-Systems/system_shell.ML => src/Pure/ML-Systems/bash.ML

tuned font handling;
explicit workaround for Apple's font manager in Java 1.6, which fails to create "IsabelleTextBold" as family member of "IsabelleText";

Standard_System.raw_exec;
more robust root.mkdirs;

Standard_System.raw_execute: optional cwd;
basic Cygwin.setup with download and unattended installation;

tuned;

separate Standard_System (Cygwin/Posix compatibility) vs. Isabelle_System (settings environment etc.);

tuned;

system shutdown hook: strict kill;

moved Library.decode_permissive_utf8 to Isabelle_System;
moved Library.with_tmp_file to Isabelle_System;
added Isabelle_System.read_file/write_file;
added Isabelle_System.system_out, with propagation of thread interrupts and process shutdown (global CTRL-C);

higher-order treatment of temporary files;

isabelle_tool: apply platform_path only once;
tuned;

slightly more paranoid cleanup of process (cf. http://kylecartmell.com/?p=9 "Five Common java.lang.Process Pitfalls");

removed unused read_file;

actually closer file reader;

tuned;

added plain read_file;

refined some Symbol operations/signatures;
added Symbol.Matcher;
flexible Scan.Lexicon.symbols, with one/many/many1 variants;

fifo: raw byte stream;
Result: fully decoded symbols and tree structure;
adapted to simplified message format;
tuned;

removed unique ids -- now in session.scala;

simplified Cygwin setup, assuming 1.7 registry layout (version 1.5 suffers from upcaseenv problem anyway);

slightly more robust and less ambitious version of install_fonts;

register_fonts: more precise error handling;

depend on Java 1.6 after all;

basic support for IsabelleText fonts;

misc tuning;

added Isabelle_System.components;

init isabelle home from existing setting or hint via system property;

fixed permissions;

proper interpretation of Cygwin.config;

some more Cygwin checks;

moved platform identification to platform.scala;
more precise discrimination, including 64bit option;

less ambitious version that works with Java 1.5;

clarified default_platform;

more detailed platform identification;

isabelle_path: slightly more liberal root pattern;

added isabelle_path;
tuned platform_path;
tuned comments;

builtin isabelle_tool for ML and Scala -- avoids excessive shell script (especially important for Cygwin);

environment: keep original HOME and PATH (required for Cygwin integrity);

added toString;

simplified IsabelleSystem.platform_path for cygwin;
eliminated ISABELLE_ROOT_JVM;
tuned;

expand_path: handle parent (..) elements;

renamed IsabelleSystem to Isabelle_System;
added expand_path;
tuned comments;
tuned;

eliminated hardwired Cygwin setup;

static IsabelleSystem.charset;
static IsabelleSystem.is_cygwin -- based on system property "os.name";
smart bootstrapping of Isabelle settings environment (via implicit or explicit ISABELLE_TOOL, or isabelle.tool property, or isabelle via PATH);
source_file: removed obsolete special treatment of "ML";
misc tuning and reorganization;

uniform (short) ids on both sides;

retrieve ML source files;

getenv_strict needs to be based on getenv (accidentally broken in 0e88d33e8d19);

fixed headers;

moved isabelle_system.scala to src/Pure/System/;

--HG--
rename : src/Pure/Tools/isabelle_system.scala => src/Pure/System/isabelle_system.scala