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

--- a/src/Pure/System/isabelle_system.scala	Tue Apr 24 15:07:49 2012 +0200
+++ b/src/Pure/System/isabelle_system.scala	Tue Apr 24 15:23:12 2012 +0200
@@ -50,9 +50,14 @@
       val standard_system = new Standard_System
       val settings =
       {
-        val env = Map(System.getenv.toList: _*) +
+        val env0 = Map(System.getenv.toList: _*) +
           ("ISABELLE_JDK_HOME" -> standard_system.this_jdk_home())
 
+        val user_home = System.getProperty("user.home")
+        val env =
+          if (user_home == null || env0.isDefinedAt("HOME")) env0
+          else env0 + ("HOME" -> user_home)
+
         val isabelle_home =
           if (this_isabelle_home != null) this_isabelle_home
           else