bin/isabelle_java

more uniform directory layout for macOS;
uniform Isabelle_app executable + lib/scripts/Isabelle_app for Linux and macOS;
proper support for Apple "Files and Folders" security via x86_64-darwin executable (which is still able to launch arm64-darwin Java);

#!/usr/bin/env bash
#
# Author: Makarius
#
# Isabelle/Java cold start -- without settings environment

if [ -L "$0" ]; then
  TARGET="$(LC_ALL=C ls -l "$0" | sed 's/.* -> //')"
  exec "$(cd "$(dirname "$0")"; cd "$(pwd -P)"; cd "$(dirname "$TARGET")"; pwd)/$(basename "$TARGET")" "$@"
fi

export ISABELLE_HOME="$(cd "$(dirname "$0")"; cd "$(pwd -P)"; cd ..; pwd)"

(
  source "$ISABELLE_HOME/lib/scripts/getsettings" || exit 2

  eval "declare -a JAVA_ARGS=($ISABELLE_JAVA_SYSTEM_OPTIONS $ISABELLE_TOOL_JAVA_OPTIONS)"

  if [ -f "$ISABELLE_HOME/src/Tools/jEdit/dist/jedit.jar" ]; then
    classpath "$ISABELLE_HOME/src/Tools/jEdit/dist/jedit.jar"
  fi

  [ -n "$CLASSPATH" ] && classpath "$CLASSPATH"

  echo "$ISABELLE_ROOT"
  echo "$CYGWIN_ROOT"
  echo "$JAVA_HOME"
  echo "$(platform_path "$ISABELLE_CLASSPATH")"
  for ARG in "${JAVA_ARGS[@]}"; do echo "$ARG"; done
) | {
  LINE_COUNT=0
  export ISABELLE_ROOT=""
  export CYGWIN_ROOT=""
  unset JAVA_HOME
  unset ISABELLE_CLASSPATH
  unset JAVA_ARGS; declare -a JAVA_ARGS

  while { unset REPLY; read -r; test "$?" = 0 -o -n "$REPLY"; }
  do
    case "$LINE_COUNT" in
      0)
        LINE_COUNT=1
        ISABELLE_ROOT="$REPLY"
        ;;
      1)
        LINE_COUNT=2
        CYGWIN_ROOT="$REPLY"
        ;;
      2)
        LINE_COUNT=3
        JAVA_HOME="$REPLY"
        ;;
      3)
        LINE_COUNT=4
        ISABELLE_CLASSPATH="$REPLY"
        ;;
      *)
        JAVA_ARGS["${#JAVA_ARGS[@]}"]="$REPLY"
        ;;
    esac
  done

  if [ -z "$JAVA_HOME" ]; then
    echo "Unknown JAVA_HOME -- Java unavailable" >&2
    exit 127
  else
    unset ISABELLE_HOME
    unset CLASSPATH
    exec "$JAVA_HOME/bin/java" "${JAVA_ARGS[@]}" \
      -classpath "$ISABELLE_CLASSPATH" "$@"
  fi
}