more explicit cygwin_root (again) -- do not rely on isabelle_home as cwd;

--- a/src/Pure/System/cygwin_init.scala	Thu Sep 05 21:11:16 2013 +0200
+++ b/src/Pure/System/cygwin_init.scala	Thu Sep 05 21:37:32 2013 +0200
@@ -100,6 +100,8 @@
 
   private def init_filesystem(isabelle_home: String, echo: String => Unit)
   {
+    val cygwin_root = isabelle_home + "\\contrib\\cygwin"
+
     def execute(args: String*): Int =
     {
       val cwd = new JFile(isabelle_home)
@@ -125,7 +127,7 @@
     echo("symlinks ...")
     val symlinks =
     {
-      val path = (new JFile("contrib\\cygwin\\isabelle\\symlinks")).toPath
+      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 =
@@ -148,10 +150,10 @@
     recover_symlinks(symlinks)
 
     echo("rebaseall ...")
-    execute("contrib\\cygwin\\bin\\dash.exe", "/isabelle/rebaseall")
+    execute(cygwin_root + "\\bin\\dash.exe", "/isabelle/rebaseall")
 
     echo("postinstall ...")
-    execute("contrib\\cygwin\\bin\\bash.exe", "/isabelle/postinstall")
+    execute(cygwin_root + "\\bin\\bash.exe", "/isabelle/postinstall")
 
     echo("init ...")
     Isabelle_System.init()

--- a/src/Pure/Tools/main.scala	Thu Sep 05 21:11:16 2013 +0200
+++ b/src/Pure/Tools/main.scala	Thu Sep 05 21:37:32 2013 +0200
@@ -47,10 +47,11 @@
             if (!(new JFile(isabelle_home)).isDirectory)
               error("Bad Isabelle home directory: " + quote(isabelle_home))
 
-            System.setProperty("cygwin.root", isabelle_home + "\\contrib\\cygwin")
+            val cygwin_root = isabelle_home + "\\contrib\\cygwin"
+            if ((new JFile(cygwin_root)).isDirectory)
+              System.setProperty("cygwin.root", cygwin_root)
 
-            val uninitialized_file =
-              new JFile(isabelle_home, "contrib\\cygwin\\isabelle\\uninitialized")
+            val uninitialized_file = new JFile(cygwin_root, "isabelle\\uninitialized")
             val uninitialized = uninitialized_file.isFile && uninitialized_file.delete
 
             if (uninitialized) Some(isabelle_home) else None