diff --git a/diffusion2d.hxx b/diffusion2d.hxx
index 2607596..22d21dd 100644
--- a/diffusion2d.hxx
+++ b/diffusion2d.hxx
@@ -3,7 +3,7 @@
 #define __NEUTRAL_DIFFUSION2D_H__
 
 #include "neutral-model.hxx"
-#include <invert_laplace.hxx>
+#include <bout/invert_laplace.hxx>
 
 class Diffusion2D : public NeutralModel {
 public:
diff --git a/div_ops.cxx b/div_ops.cxx
index d24d4f1..0d9b4ee 100644
--- a/div_ops.cxx
+++ b/div_ops.cxx
@@ -27,11 +27,11 @@
 
 #include <bout/assert.hxx>
 #include <bout/mesh.hxx>
-#include <derivs.hxx>
-#include <difops.hxx>
-#include <globals.hxx>
-#include <output.hxx>
-#include <utils.hxx>
+#include <bout/derivs.hxx>
+#include <bout/difops.hxx>
+#include <bout/globals.hxx>
+#include <bout/output.hxx>
+#include <bout/utils.hxx>
 
 #include <bout/index_derivs.hxx>
 
diff --git a/div_ops.hxx b/div_ops.hxx
index 555cda8..4d09d20 100644
--- a/div_ops.hxx
+++ b/div_ops.hxx
@@ -26,8 +26,8 @@
 #ifndef __DIV_OPS_H__
 #define __DIV_OPS_H__
 
-#include <field3d.hxx>
-#include <vector3d.hxx>
+#include <bout/field3d.hxx>
+#include <bout/vector3d.hxx>
 
 class CustomStencil {
 public:
diff --git a/hermes-2.cxx b/hermes-2.cxx
index 555cd57..f09ce8a 100644
--- a/hermes-2.cxx
+++ b/hermes-2.cxx
@@ -21,13 +21,13 @@
 */
 #include "hermes-2.hxx"
 
-#include <derivs.hxx>
-#include <field_factory.hxx>
-#include <initialprofiles.hxx>
+#include <bout/derivs.hxx>
+#include <bout/field_factory.hxx>
+#include <bout/initialprofiles.hxx>
 
-#include <invert_parderiv.hxx>
-#include "parallel_boundary_region.hxx"
-#include "boundary_region.hxx"
+#include <bout/invert_parderiv.hxx>
+#include <bout/parallel_boundary_region.hxx>
+#include <bout/boundary_region.hxx>
 
 #include "div_ops.hxx"
 #include "loadmetric.hxx"
diff --git a/hermes-2.hxx b/hermes-2.hxx
index 9b2c428..ff5c05e 100644
--- a/hermes-2.hxx
+++ b/hermes-2.hxx
@@ -26,11 +26,11 @@ class Hermes;
 
 #include <bout/physicsmodel.hxx>
 
-#include <invert_laplace.hxx>
+#include <bout/invert_laplace.hxx>
 #include <bout/invert/laplacexy.hxx>
 #include <bout/invert/laplacexz.hxx>
 #include <bout/constants.hxx>
-#include <mask.hxx>
+#include <bout/mask.hxx>
 
 #include "neutral-model.hxx"
 
diff --git a/loadmetric.cxx b/loadmetric.cxx
index a5400b8..033e3e5 100644
--- a/loadmetric.cxx
+++ b/loadmetric.cxx
@@ -1,7 +1,7 @@
-#include <globals.hxx>
-#include <output.hxx>
-#include <utils.hxx>
-#include <field2d.hxx>
+#include <bout/globals.hxx>
+#include <bout/output.hxx>
+#include <bout/utils.hxx>
+#include <bout/field2d.hxx>
 #include <bout/mesh.hxx>
 
 #include "loadmetric.hxx"
diff --git a/loadmetric.hxx b/loadmetric.hxx
index 7020e7c..d6258ee 100644
--- a/loadmetric.hxx
+++ b/loadmetric.hxx
@@ -2,7 +2,7 @@
 #ifndef __LOADMETRIC_H__
 #define __LOADMETRIC_H__
 
-#include <bout_types.hxx>
+#include <bout/bout_types.hxx>
 
 void LoadMetric(BoutReal Lnorm, BoutReal Bnorm);
 
diff --git a/neutral-model.hxx b/neutral-model.hxx
index bca353f..7ee997f 100644
--- a/neutral-model.hxx
+++ b/neutral-model.hxx
@@ -5,8 +5,8 @@
 #ifndef __NEUTRAL_MODEL_H__
 #define __NEUTRAL_MODEL_H__
 
-#include <field3d.hxx>
-#include <options.hxx>
+#include <bout/field3d.hxx>
+#include <bout/options.hxx>
 #include <bout/solver.hxx>
 #include <bout/mesh.hxx>
 
diff --git a/radiation.cxx b/radiation.cxx
index 85921ac..bfa813e 100644
--- a/radiation.cxx
+++ b/radiation.cxx
@@ -1,7 +1,7 @@
-#include <boutexception.hxx>
-#include <globals.hxx> // for mesh object
-#include <output.hxx>
-#include <utils.hxx>
+#include <bout/boutexception.hxx>
+#include <bout/globals.hxx> // for mesh object
+#include <bout/output.hxx>
+#include <bout/utils.hxx>
 
 #include "radiation.hxx"
 
diff --git a/radiation.hxx b/radiation.hxx
index 837719f..7c607e9 100644
--- a/radiation.hxx
+++ b/radiation.hxx
@@ -2,8 +2,8 @@
 #ifndef __RADIATION_H__
 #define __RADIATION_H__
 
-#include <field3d.hxx>
-#include <bout_types.hxx>
+#include <bout/field3d.hxx>
+#include <bout/bout_types.hxx>
 
 #include <vector>
 #include <cmath>