diff --git a/gtsam/inference/BayesTree-inl.h b/gtsam/inference/BayesTree-inl.h
index 6178b6446..24f57cc55 100644
--- a/gtsam/inference/BayesTree-inl.h
+++ b/gtsam/inference/BayesTree-inl.h
@@ -21,7 +21,7 @@
 
 #include <gtsam/base/FastSet.h>
 #include <gtsam/inference/BayesTree.h>
-#include <gtsam/inference/inference-inl.h>
+#include <gtsam/inference/inference.h>
 #include <gtsam/inference/GenericSequentialSolver-inl.h>
 
 #include <iostream>
diff --git a/gtsam/inference/GenericMultifrontalSolver-inl.h b/gtsam/inference/GenericMultifrontalSolver-inl.h
index eab48f108..6bf8c55a9 100644
--- a/gtsam/inference/GenericMultifrontalSolver-inl.h
+++ b/gtsam/inference/GenericMultifrontalSolver-inl.h
@@ -22,7 +22,6 @@
 #include <gtsam/inference/FactorBase-inl.h>
 #include <gtsam/inference/JunctionTree-inl.h>
 #include <gtsam/inference/BayesNet-inl.h>
-#include <gtsam/inference/inference-inl.h>
 
 #include <boost/foreach.hpp>
 
diff --git a/gtsam/inference/GenericSequentialSolver-inl.h b/gtsam/inference/GenericSequentialSolver-inl.h
index 2f6a3ac73..3c2547ead 100644
--- a/gtsam/inference/GenericSequentialSolver-inl.h
+++ b/gtsam/inference/GenericSequentialSolver-inl.h
@@ -22,7 +22,6 @@
 #include <gtsam/inference/FactorBase-inl.h>
 #include <gtsam/inference/EliminationTree-inl.h>
 #include <gtsam/inference/BayesNet-inl.h>
-#include <gtsam/inference/inference-inl.h>
 
 #include <boost/foreach.hpp>
 
diff --git a/gtsam/inference/JunctionTree-inl.h b/gtsam/inference/JunctionTree-inl.h
index 209fd484f..b4c61dfa1 100644
--- a/gtsam/inference/JunctionTree-inl.h
+++ b/gtsam/inference/JunctionTree-inl.h
@@ -23,7 +23,6 @@
 #include <gtsam/inference/SymbolicFactorGraph.h>
 #include <gtsam/inference/BayesTree-inl.h>
 #include <gtsam/inference/JunctionTree.h>
-#include <gtsam/inference/inference-inl.h>
 #include <gtsam/inference/VariableSlots.h>
 #include <gtsam/inference/EliminationTree-inl.h>
 #include <gtsam/inference/ClusterTree-inl.h>
diff --git a/gtsam/inference/Makefile.am b/gtsam/inference/Makefile.am
index 6bc2db28e..6603328db 100644
--- a/gtsam/inference/Makefile.am
+++ b/gtsam/inference/Makefile.am
@@ -24,7 +24,6 @@ check_PROGRAMS += tests/testSymbolicBayesNet tests/testVariableIndex tests/testV
 
 # Inference
 headers += GenericMultifrontalSolver.h GenericMultifrontalSolver-inl.h GenericSequentialSolver.h GenericSequentialSolver-inl.h
-headers += inference-inl.h
 sources += inference.cpp VariableSlots.cpp Permutation.cpp VariableIndex.cpp
 sources += IndexFactor.cpp IndexConditional.cpp
 headers += graph.h graph-inl.h
@@ -35,6 +34,7 @@ headers += EliminationTree.h EliminationTree-inl.h
 headers += BayesNet.h BayesNet-inl.h
 headers += BayesTree.h BayesTree-inl.h
 headers += ISAM.h ISAM-inl.h
+check_PROGRAMS += tests/testInference
 check_PROGRAMS += tests/testFactorGraph
 check_PROGRAMS += tests/testFactorGraph
 check_PROGRAMS += tests/testBayesTree 
diff --git a/gtsam/inference/SymbolicFactorGraph.cpp b/gtsam/inference/SymbolicFactorGraph.cpp
index 31b44523d..10c35f752 100644
--- a/gtsam/inference/SymbolicFactorGraph.cpp
+++ b/gtsam/inference/SymbolicFactorGraph.cpp
@@ -23,7 +23,6 @@
 #include <gtsam/inference/SymbolicFactorGraph.h>
 #include <gtsam/inference/BayesNet-inl.h>
 #include <gtsam/inference/IndexFactor.h>
-#include <gtsam/inference/inference-inl.h>
 #include <gtsam/inference/EliminationTree-inl.h>
 
 using namespace std;
diff --git a/gtsam/inference/inference-inl.h b/gtsam/inference/inference-inl.h
deleted file mode 100644
index 859fd9797..000000000
--- a/gtsam/inference/inference-inl.h
+++ /dev/null
@@ -1,26 +0,0 @@
-/* ----------------------------------------------------------------------------
-
- * GTSAM Copyright 2010, Georgia Tech Research Corporation, 
- * Atlanta, Georgia 30332-0415
- * All Rights Reserved
- * Authors: Frank Dellaert, et al. (see THANKS for the full author list)
-
- * See LICENSE for the license information
-
- * -------------------------------------------------------------------------- */
-
-/**
- * @file   inference-inl.h
- * @brief  inference template definitions
- * @author Frank Dellaert, Richard Roberts
- */
-
-#pragma once
-
-#include <gtsam/inference/inference.h>
-
-using namespace std;
-
-namespace gtsam {
-
-} // namespace gtsam
diff --git a/gtsam/inference/inference.cpp b/gtsam/inference/inference.cpp
index a3a81e7a4..fe4b3044e 100644
--- a/gtsam/inference/inference.cpp
+++ b/gtsam/inference/inference.cpp
@@ -15,14 +15,18 @@
  * @author Frank Dellaert, Richard Roberts
  */
 
-#include <gtsam/inference/inference-inl.h>
+#include <gtsam/inference/inference.h>
 #include <gtsam/inference/SymbolicFactorGraph.h>
 
 #include <boost/format.hpp>
 #include <stdexcept>
+#include <iostream>
+#include <vector>
 
 #include <ccolamd.h>
 
+using namespace std;
+
 namespace gtsam {
 
 Permutation::shared_ptr Inference::PermutationCOLAMD_(const VariableIndex& variableIndex, std::vector<int>& cmember) {
@@ -73,7 +77,10 @@ Permutation::shared_ptr Inference::PermutationCOLAMD_(const VariableIndex& varia
   // Convert elimination ordering in p to an ordering
   Permutation::shared_ptr permutation(new Permutation(nVars));
   for (Index j = 0; j < nVars; j++) {
-    permutation->operator[](j) = p[j];
+//    if(p[j] == -1)
+//      permutation->operator[](j) = j;
+//    else
+      permutation->operator[](j) = p[j];
     if(debug) cout << "COLAMD:  " << j << "->" << p[j] << endl;
   }
   if(debug) cout << "COLAMD:  p[" << nVars << "] = " << p[nVars] << endl;
diff --git a/gtsam/inference/tests/testInference.cpp b/gtsam/inference/tests/testInference.cpp
new file mode 100644
index 000000000..c7f80282d
--- /dev/null
+++ b/gtsam/inference/tests/testInference.cpp
@@ -0,0 +1,47 @@
+/* ----------------------------------------------------------------------------
+
+ * GTSAM Copyright 2010, Georgia Tech Research Corporation,
+ * Atlanta, Georgia 30332-0415
+ * All Rights Reserved
+ * Authors: Frank Dellaert, et al. (see THANKS for the full author list)
+
+ * See LICENSE for the license information
+
+ * -------------------------------------------------------------------------- */
+
+/**
+ * @file    testInference.cpp
+ * @brief   
+ * @author  Richard Roberts
+ * @created Dec 6, 2010
+ */
+
+#include <CppUnitLite/TestHarness.h>
+
+#include <gtsam/inference/inference.h>
+#include <gtsam/inference/VariableIndex.h>
+#include <gtsam/inference/SymbolicFactorGraph.h>
+
+using namespace gtsam;
+
+/* ************************************************************************* */
+TEST(Inference, UnobservedVariables) {
+  SymbolicFactorGraph sfg;
+
+  // Create a factor graph that skips some variables
+  sfg.push_factor(0,1);
+  sfg.push_factor(1,3);
+  sfg.push_factor(3,5);
+
+  VariableIndex variableIndex(sfg);
+
+  Permutation::shared_ptr colamd(Inference::PermutationCOLAMD(variableIndex));
+
+  colamd->print("colamd: ");
+}
+
+/* ************************************************************************* */
+int main() {
+  TestResult tr;
+  return TestRegistry::runAllTests(tr);
+}
diff --git a/gtsam/inference/tests/testOrdering.cpp b/gtsam/inference/tests/testOrdering.cpp
deleted file mode 100644
index b25593aa1..000000000
--- a/gtsam/inference/tests/testOrdering.cpp
+++ /dev/null
@@ -1,53 +0,0 @@
-/* ----------------------------------------------------------------------------
-
- * GTSAM Copyright 2010, Georgia Tech Research Corporation, 
- * Atlanta, Georgia 30332-0415
- * All Rights Reserved
- * Authors: Frank Dellaert, et al. (see THANKS for the full author list)
-
- * See LICENSE for the license information
-
- * -------------------------------------------------------------------------- */
-
-/**
- * @file testOrdering.cpp
- * @author Alex Cunningham
- */
-
-#include <boost/assign/std/list.hpp> // for operator +=
-using namespace boost::assign;
-
-#include <CppUnitLite/TestHarness.h>
-
-// Magically turn strings into Symbols
-#define GTSAM_MAGIC_KEY
-
-#include <gtsam/inference/Ordering.h>
-
-using namespace std;
-using namespace gtsam;
-
-/* ************************************************************************* */
-TEST ( Ordering, subtract )
-{
-	Ordering init, delta;
-	init += "a", "b", "c", "d", "e";
-	CHECK(assert_equal(init.subtract(delta), init));
-
-	delta += "b";
-	Ordering expected1;
-	expected1 += "a", "c", "d", "e";
-	CHECK(assert_equal(init.subtract(delta), expected1));
-
-	delta += "e";
-	Ordering expected2;
-	expected2 += "a", "c", "d";
-	CHECK(assert_equal(init.subtract(delta), expected2));
-}
-
-/* ************************************************************************* */
-int main() {
-	TestResult tr;
-	return TestRegistry::runAllTests(tr);
-}
-/* ************************************************************************* */
diff --git a/gtsam/linear/GaussianFactor.h b/gtsam/linear/GaussianFactor.h
index 4159690e5..b43434a94 100644
--- a/gtsam/linear/GaussianFactor.h
+++ b/gtsam/linear/GaussianFactor.h
@@ -47,8 +47,6 @@
 
 namespace gtsam {
 
-  class GaussianFactorGraph;
-
   /** A map from key to dimension, useful in various contexts */
   typedef std::map<Index, size_t> Dimensions;
 
diff --git a/gtsam/linear/GaussianFactorGraph.cpp b/gtsam/linear/GaussianFactorGraph.cpp
index ddcad80ea..ede5571a8 100644
--- a/gtsam/linear/GaussianFactorGraph.cpp
+++ b/gtsam/linear/GaussianFactorGraph.cpp
@@ -26,7 +26,6 @@
 
 #include <gtsam/linear/GaussianFactorGraph.h>
 #include <gtsam/inference/FactorGraph-inl.h>
-#include <gtsam/inference/inference-inl.h>
 #include <gtsam/linear/iterative.h>
 
 
diff --git a/gtsam/linear/tests/timeFactorOverhead.cpp b/gtsam/linear/tests/timeFactorOverhead.cpp
index b0440b08b..c25e069f1 100644
--- a/gtsam/linear/tests/timeFactorOverhead.cpp
+++ b/gtsam/linear/tests/timeFactorOverhead.cpp
@@ -18,7 +18,6 @@
 
 #include <gtsam/linear/GaussianFactorGraph.h>
 #include <gtsam/linear/SharedDiagonal.h>
-#include <gtsam/inference/inference-inl.h>
 #include <gtsam/inference/EliminationTree-inl.h>
 
 #include <boost/random.hpp>
diff --git a/gtsam/nonlinear/NonlinearFactorGraph-inl.h b/gtsam/nonlinear/NonlinearFactorGraph-inl.h
index cb0ed0288..264ab9430 100644
--- a/gtsam/nonlinear/NonlinearFactorGraph-inl.h
+++ b/gtsam/nonlinear/NonlinearFactorGraph-inl.h
@@ -23,7 +23,7 @@
 #include <gtsam/linear/GaussianFactorGraph.h>
 #include <gtsam/nonlinear/NonlinearFactorGraph.h>
 #include <gtsam/inference/FactorGraph-inl.h>
-#include <gtsam/inference/inference-inl.h>
+#include <gtsam/inference/inference.h>
 
 #define INSTANTIATE_NONLINEAR_FACTOR_GRAPH(C) \
   INSTANTIATE_FACTOR_GRAPH(NonlinearFactor<C>); \
diff --git a/gtsam/slam/saveGraph.cpp b/gtsam/slam/saveGraph.cpp
index 2c9dcf7c1..ac390b1e5 100644
--- a/gtsam/slam/saveGraph.cpp
+++ b/gtsam/slam/saveGraph.cpp
@@ -21,7 +21,6 @@
 #include <gtsam/geometry/Point2.h>
 #include <gtsam/inference/SymbolicFactorGraph.h>
 #include <gtsam/inference/SymbolicBayesNet.h>
-#include <gtsam/inference/inference-inl.h>
 #include <gtsam/nonlinear/LieValues-inl.h>
 
 using namespace std;
diff --git a/tests/testGaussianFactor.cpp b/tests/testGaussianFactor.cpp
index e7761a1e7..e947b6707 100644
--- a/tests/testGaussianFactor.cpp
+++ b/tests/testGaussianFactor.cpp
@@ -30,7 +30,6 @@ using namespace boost::assign;
 
 #include <gtsam/base/Matrix.h>
 #include <gtsam/linear/GaussianConditional.h>
-#include <gtsam/inference/inference-inl.h>
 #include <gtsam/slam/smallExample.h>
 #include <gtsam/nonlinear/Ordering.h>