diff -r b18f83985215 -r e00e1bf23d03 src/Pure/System/cygwin.scala
--- a/src/Pure/System/cygwin.scala	Wed Sep 30 14:49:39 2015 +0200
+++ b/src/Pure/System/cygwin.scala	Wed Sep 30 20:02:39 2015 +0200
@@ -15,73 +15,51 @@
 
 object Cygwin
 {
-  /** Cygwin init (e.g. after extraction via 7zip) **/
-
-  def init()
-  {
-    val isabelle_home0 = System.getenv("ISABELLE_HOME")
-    if (isabelle_home0 == null || isabelle_home0 == "") {
+  /* init (e.g. after extraction via 7zip) */
 
-      /* isabelle_home */
-
-      val isabelle_home = System.getProperty("isabelle.home", "")
-
-      if (isabelle_home == "")
-        error("Unknown Isabelle home directory")
-
-      if (!(new JFile(isabelle_home)).isDirectory)
-        error("Bad Isabelle home directory: " + quote(isabelle_home))
+  def init(isabelle_home: String, cygwin_root: String)
+  {
+    require(Platform.is_windows)
 
-      def execute(args: String*)
-      {
-        val cwd = new JFile(isabelle_home)
-        val env = Map("CYGWIN" -> "nodosfilewarning")
-        val proc = Isabelle_System.raw_execute(cwd, env, true, args: _*)
-        val (output, rc) = Isabelle_System.process_output(proc)
-        if (rc != 0) error(output)
-      }
+    def execute(args: String*)
+    {
+      val cwd = new JFile(isabelle_home)
+      val env = Map("CYGWIN" -> "nodosfilewarning")
+      val proc = Isabelle_System.raw_execute(cwd, env, true, args: _*)
+      val (output, rc) = Isabelle_System.process_output(proc)
+      if (rc != 0) error(output)
+    }
 
-
-      /* cygwin_root */
-
-      val cygwin_root = isabelle_home + "\\contrib\\cygwin"
-      if ((new JFile(cygwin_root)).isDirectory)
-        System.setProperty("cygwin.root", cygwin_root)
-
+    val uninitialized_file = new JFile(cygwin_root, "isabelle\\uninitialized")
+    val uninitialized = uninitialized_file.isFile && uninitialized_file.delete
 
-      /* init */
-
-      val uninitialized_file = new JFile(cygwin_root, "isabelle\\uninitialized")
-      val uninitialized = uninitialized_file.isFile && uninitialized_file.delete
+    if (uninitialized) {
+      val symlinks =
+      {
+        val path = (new JFile(cygwin_root + "\\isabelle\\symlinks")).toPath
+        Files.readAllLines(path, UTF8.charset).toArray.toList.asInstanceOf[List[String]]
+      }
+      @tailrec def recover_symlinks(list: List[String]): Unit =
+      {
+        list match {
+          case Nil | List("") =>
+          case link :: content :: rest =>
+            val path = (new JFile(isabelle_home, link)).toPath
 
-      if (uninitialized) {
-        val symlinks =
-        {
-          val path = (new JFile(cygwin_root + "\\isabelle\\symlinks")).toPath
-          Files.readAllLines(path, UTF8.charset).toArray.toList.asInstanceOf[List[String]]
+            val writer = Files.newBufferedWriter(path, UTF8.charset)
+            try { writer.write("!<symlink>" + content + "\u0000") }
+            finally { writer.close }
+
+            Files.setAttribute(path, "dos:system", true)
+
+            recover_symlinks(rest)
+          case _ => error("Unbalanced symlinks list")
         }
-        @tailrec def recover_symlinks(list: List[String]): Unit =
-        {
-          list match {
-            case Nil | List("") =>
-            case link :: content :: rest =>
-              val path = (new JFile(isabelle_home, link)).toPath
-
-              val writer = Files.newBufferedWriter(path, UTF8.charset)
-              try { writer.write("!<symlink>" + content + "\u0000") }
-              finally { writer.close }
+      }
+      recover_symlinks(symlinks)
 
-              Files.setAttribute(path, "dos:system", true)
-
-              recover_symlinks(rest)
-            case _ => error("Unbalanced symlinks list")
-          }
-        }
-        recover_symlinks(symlinks)
-
-        execute(cygwin_root + "\\bin\\dash.exe", "/isabelle/rebaseall")
-        execute(cygwin_root + "\\bin\\bash.exe", "/isabelle/postinstall")
-      }
+      execute(cygwin_root + "\\bin\\dash.exe", "/isabelle/rebaseall")
+      execute(cygwin_root + "\\bin\\bash.exe", "/isabelle/postinstall")
     }
   }
 }