diff -U 3 -dHrN M2source/Macaulay2/packages/FourTiTwo.m2 M2source.patch/Macaulay2/packages/FourTiTwo.m2
--- M2source/Macaulay2/packages/FourTiTwo.m2	2011-09-22 14:36:51.000000000 +0100
+++ M2source.patch/Macaulay2/packages/FourTiTwo.m2	2011-09-24 21:24:12.000000000 +0100
@@ -47,7 +47,7 @@
 
 path'4ti2 = (options FourTiTwo).Configuration#"path"
 -- NOTE: the absolute path should be put into the .init file for 4ti2 inside the .Macaulay2 directory.
-if path'4ti2 == "" then path'4ti2 = prefixDirectory | currentLayout#"programs"
+if path'4ti2 == "" then path'4ti2 = "/usr/bin/"
 
 getFilename = () -> (
      filename := temporaryFileName();
diff -U 3 -dHrN M2source/Macaulay2/packages/gfanInterface.m2 M2source.patch/Macaulay2/packages/gfanInterface.m2
--- M2source/Macaulay2/packages/gfanInterface.m2	2011-05-14 12:00:59.000000000 +0100
+++ M2source.patch/Macaulay2/packages/gfanInterface.m2	2011-09-24 21:24:12.000000000 +0100
@@ -25,7 +25,7 @@
      }
 
 gfan'path = gfanInterface#Options#Configuration#"path"
-if gfan'path == "" then gfan'path = prefixDirectory | currentLayout#"programs"
+if gfan'path == "" then gfan'path = "/usr/bin/"
 if instance(gfan'path, String) then gfan'path = {gfan'path}
 if not instance(gfan'path,List) then error "expected configuration option gfan'path to be a list of strings or a string"
 gfan'path = join(
diff -U 3 -dHrN M2source/Macaulay2/packages/NautyGraphs.m2 M2source.patch/Macaulay2/packages/NautyGraphs.m2
--- M2source/Macaulay2/packages/NautyGraphs.m2	2011-08-26 11:05:30.000000000 +0100
+++ M2source.patch/Macaulay2/packages/NautyGraphs.m2	2011-09-24 21:25:53.000000000 +0100
@@ -32,7 +32,7 @@
 -- Check the ~/.Macaulay2/init-NautyGraphs.m2 file for the absolute path.
 -- If it's not there, then use the M2-Programs directory.
 nauty'path = (options NautyGraphs).Configuration#"path";
-if nauty'path == "" then nauty'path = prefixDirectory | currentLayout#"programs";
+if nauty'path == "" then nauty'path = "/usr/bin/";
 
 -------------------
 -- Exports
diff -U 3 -dHrN M2source/Macaulay2/packages/Nauty.m2 M2source.patch/Macaulay2/packages/Nauty.m2
--- M2source/Macaulay2/packages/Nauty.m2	2011-08-26 11:05:30.000000000 +0100
+++ M2source.patch/Macaulay2/packages/Nauty.m2	2011-09-24 21:24:12.000000000 +0100
@@ -48,7 +48,8 @@
 -- Check the ~/.Macaulay2/init-Nauty.m2 file for the absolute path.
 -- If it's not there, then use the M2-Programs directory.
 nauty'path = (options Nauty).Configuration#"path";
-if nauty'path == "" then nauty'path = prefixDirectory | currentLayout#"programs";
+if nauty'path == "" then nauty'path = "/usr/bin/";
+
 
 -------------------
 -- Exports
diff -U 3 -dHrN M2source/Macaulay2/packages/Normaliz.m2 M2source.patch/Macaulay2/packages/Normaliz.m2
--- M2source/Macaulay2/packages/Normaliz.m2	2011-05-25 16:47:50.000000000 +0100
+++ M2source.patch/Macaulay2/packages/Normaliz.m2	2011-09-24 21:24:12.000000000 +0100
@@ -166,7 +166,7 @@
         nmzExec="normaliz";
     );
 --    return nmzExec;
-    return prefixDirectory | currentLayout#"programs" | nmzExec;
+    return "/usr/bin/" | nmzExec;
 );
 
 
diff -U 3 -dHrN M2source/Macaulay2/packages/StatePolytope.m2 M2source.patch/Macaulay2/packages/StatePolytope.m2
--- M2source/Macaulay2/packages/StatePolytope.m2	2010-09-10 16:47:20.000000000 +0100
+++ M2source.patch/Macaulay2/packages/StatePolytope.m2	2011-09-24 21:24:12.000000000 +0100
@@ -31,7 +31,7 @@
 
 
 gfanCommand = (options StatePolytope)#Configuration#"gfan command"
-if gfanCommand === "gfan" then gfanCommand = prefixDirectory | currentLayout#"programs" | gfanCommand
+if gfanCommand === "gfan" then gfanCommand = "/usr/bin/" | gfanCommand
 gfanCommand = "!" | gfanCommand
 
 --The next two functions print out the ring and the ideal in the format required by gfan