diff --git a/include/boundary_factory.hxx b/include/boundary_factory.hxx
deleted file mode 100644
index abbead8fc4..0000000000
--- a/include/boundary_factory.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "boundary_factory.hxx" has moved to "bout/boundary_factory.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/boundary_factory.hxx"
diff --git a/include/boundary_op.hxx b/include/boundary_op.hxx
deleted file mode 100644
index c96310f2d4..0000000000
--- a/include/boundary_op.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "boundary_op.hxx" has moved to "bout/boundary_op.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/boundary_op.hxx"
diff --git a/include/boundary_region.hxx b/include/boundary_region.hxx
deleted file mode 100644
index f487e88aeb..0000000000
--- a/include/boundary_region.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "boundary_region.hxx" has moved to "bout/boundary_region.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/boundary_region.hxx"
diff --git a/include/boundary_standard.hxx b/include/boundary_standard.hxx
deleted file mode 100644
index b7f17cf363..0000000000
--- a/include/boundary_standard.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "boundary_standard.hxx" has moved to "bout/boundary_standard.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/boundary_standard.hxx"
diff --git a/include/bout.hxx b/include/bout.hxx
deleted file mode 100644
index 926f035d2f..0000000000
--- a/include/bout.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "bout.hxx" has moved to "bout/bout.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/bout.hxx"
diff --git a/include/bout_types.hxx b/include/bout_types.hxx
deleted file mode 100644
index e6048eb885..0000000000
--- a/include/bout_types.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "bout_types.hxx" has moved to "bout/bout_types.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/bout_types.hxx"
diff --git a/include/boutcomm.hxx b/include/boutcomm.hxx
deleted file mode 100644
index 256df49c4f..0000000000
--- a/include/boutcomm.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "boutcomm.hxx" has moved to "bout/boutcomm.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/boutcomm.hxx"
diff --git a/include/boutexception.hxx b/include/boutexception.hxx
deleted file mode 100644
index 9189babfb3..0000000000
--- a/include/boutexception.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "boutexception.hxx" has moved to "bout/boutexception.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/boutexception.hxx"
diff --git a/include/cyclic_reduction.hxx b/include/cyclic_reduction.hxx
deleted file mode 100644
index 3ff098b062..0000000000
--- a/include/cyclic_reduction.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "cyclic_reduction.hxx" has moved to "bout/cyclic_reduction.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/cyclic_reduction.hxx"
diff --git a/include/dcomplex.hxx b/include/dcomplex.hxx
deleted file mode 100644
index a91c5485bf..0000000000
--- a/include/dcomplex.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "dcomplex.hxx" has moved to "bout/dcomplex.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/dcomplex.hxx"
diff --git a/include/derivs.hxx b/include/derivs.hxx
deleted file mode 100644
index d0a6eb5831..0000000000
--- a/include/derivs.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "derivs.hxx" has moved to "bout/derivs.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/derivs.hxx"
diff --git a/include/difops.hxx b/include/difops.hxx
deleted file mode 100644
index a61d9712a9..0000000000
--- a/include/difops.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "difops.hxx" has moved to "bout/difops.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/difops.hxx"
diff --git a/include/fft.hxx b/include/fft.hxx
deleted file mode 100644
index d67b257388..0000000000
--- a/include/fft.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "fft.hxx" has moved to "bout/fft.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/fft.hxx"
diff --git a/include/field.hxx b/include/field.hxx
deleted file mode 100644
index a2fcb2464e..0000000000
--- a/include/field.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "field.hxx" has moved to "bout/field.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/field.hxx"
diff --git a/include/field2d.hxx b/include/field2d.hxx
deleted file mode 100644
index 3b148b3a50..0000000000
--- a/include/field2d.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "field2d.hxx" has moved to "bout/field2d.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/field2d.hxx"
diff --git a/include/field3d.hxx b/include/field3d.hxx
deleted file mode 100644
index 300cec057b..0000000000
--- a/include/field3d.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "field3d.hxx" has moved to "bout/field3d.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/field3d.hxx"
diff --git a/include/field_data.hxx b/include/field_data.hxx
deleted file mode 100644
index 90f5c96c40..0000000000
--- a/include/field_data.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "field_data.hxx" has moved to "bout/field_data.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/field_data.hxx"
diff --git a/include/field_factory.hxx b/include/field_factory.hxx
deleted file mode 100644
index c6302ee298..0000000000
--- a/include/field_factory.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "field_factory.hxx" has moved to "bout/field_factory.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/field_factory.hxx"
diff --git a/include/fieldperp.hxx b/include/fieldperp.hxx
deleted file mode 100644
index 1994e53060..0000000000
--- a/include/fieldperp.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "fieldperp.hxx" has moved to "bout/fieldperp.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/fieldperp.hxx"
diff --git a/include/globals.hxx b/include/globals.hxx
deleted file mode 100644
index f07488c10c..0000000000
--- a/include/globals.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "globals.hxx" has moved to "bout/globals.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/globals.hxx"
diff --git a/include/gyro_average.hxx b/include/gyro_average.hxx
deleted file mode 100644
index c0d454eb50..0000000000
--- a/include/gyro_average.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "gyro_average.hxx" has moved to "bout/gyro_average.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/gyro_average.hxx"
diff --git a/include/initialprofiles.hxx b/include/initialprofiles.hxx
deleted file mode 100644
index 7bc1595261..0000000000
--- a/include/initialprofiles.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "initialprofiles.hxx" has moved to "bout/initialprofiles.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/initialprofiles.hxx"
diff --git a/include/interpolation.hxx b/include/interpolation.hxx
deleted file mode 100644
index 80ad60b4e4..0000000000
--- a/include/interpolation.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "interpolation.hxx" has moved to "bout/interpolation.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/interpolation.hxx"
diff --git a/include/interpolation_xz.hxx b/include/interpolation_xz.hxx
deleted file mode 100644
index 8845e34b80..0000000000
--- a/include/interpolation_xz.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "interpolation_xz.hxx" has moved to "bout/interpolation_xz.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/interpolation_xz.hxx"
diff --git a/include/interpolation_z.hxx b/include/interpolation_z.hxx
deleted file mode 100644
index a88b486026..0000000000
--- a/include/interpolation_z.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "interpolation_z.hxx" has moved to "bout/interpolation_z.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/interpolation_z.hxx"
diff --git a/include/invert_laplace.hxx b/include/invert_laplace.hxx
deleted file mode 100644
index fbb04acaf1..0000000000
--- a/include/invert_laplace.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "invert_laplace.hxx" has moved to "bout/invert_laplace.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/invert_laplace.hxx"
diff --git a/include/invert_parderiv.hxx b/include/invert_parderiv.hxx
deleted file mode 100644
index 81a8ca4f49..0000000000
--- a/include/invert_parderiv.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "invert_parderiv.hxx" has moved to "bout/invert_parderiv.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/invert_parderiv.hxx"
diff --git a/include/lapack_routines.hxx b/include/lapack_routines.hxx
deleted file mode 100644
index 97fa2c6be9..0000000000
--- a/include/lapack_routines.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "lapack_routines.hxx" has moved to "bout/lapack_routines.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/lapack_routines.hxx"
diff --git a/include/mask.hxx b/include/mask.hxx
deleted file mode 100644
index cbeab65d85..0000000000
--- a/include/mask.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "mask.hxx" has moved to "bout/mask.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/mask.hxx"
diff --git a/include/msg_stack.hxx b/include/msg_stack.hxx
deleted file mode 100644
index 2503961748..0000000000
--- a/include/msg_stack.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "msg_stack.hxx" has moved to "bout/msg_stack.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/msg_stack.hxx"
diff --git a/include/multiostream.hxx b/include/multiostream.hxx
deleted file mode 100644
index 7e7101aad0..0000000000
--- a/include/multiostream.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "multiostream.hxx" has moved to "bout/multiostream.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/multiostream.hxx"
diff --git a/include/options.hxx b/include/options.hxx
deleted file mode 100644
index 4693422c13..0000000000
--- a/include/options.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "options.hxx" has moved to "bout/options.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/options.hxx"
diff --git a/include/optionsreader.hxx b/include/optionsreader.hxx
deleted file mode 100644
index 2c0f8344bf..0000000000
--- a/include/optionsreader.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "optionsreader.hxx" has moved to "bout/optionsreader.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/optionsreader.hxx"
diff --git a/include/output.hxx b/include/output.hxx
deleted file mode 100644
index 7eebcad478..0000000000
--- a/include/output.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "output.hxx" has moved to "bout/output.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/output.hxx"
diff --git a/include/parallel_boundary_op.hxx b/include/parallel_boundary_op.hxx
deleted file mode 100644
index e82a88d98f..0000000000
--- a/include/parallel_boundary_op.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "parallel_boundary_op.hxx" has moved to "bout/parallel_boundary_op.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/parallel_boundary_op.hxx"
diff --git a/include/parallel_boundary_region.hxx b/include/parallel_boundary_region.hxx
deleted file mode 100644
index dee2277007..0000000000
--- a/include/parallel_boundary_region.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "parallel_boundary_region.hxx" has moved to "bout/parallel_boundary_region.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/parallel_boundary_region.hxx"
diff --git a/include/smoothing.hxx b/include/smoothing.hxx
deleted file mode 100644
index b1a36adfb2..0000000000
--- a/include/smoothing.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "smoothing.hxx" has moved to "bout/smoothing.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/smoothing.hxx"
diff --git a/include/sourcex.hxx b/include/sourcex.hxx
deleted file mode 100644
index e09f3e89e4..0000000000
--- a/include/sourcex.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "sourcex.hxx" has moved to "bout/sourcex.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/sourcex.hxx"
diff --git a/include/stencils.hxx b/include/stencils.hxx
deleted file mode 100644
index fc877f3e1c..0000000000
--- a/include/stencils.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "stencils.hxx" has moved to "bout/stencils.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/stencils.hxx"
diff --git a/include/unused.hxx b/include/unused.hxx
deleted file mode 100644
index fa5ea7b6d1..0000000000
--- a/include/unused.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "unused.hxx" has moved to "bout/unused.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/unused.hxx"
diff --git a/include/utils.hxx b/include/utils.hxx
deleted file mode 100644
index d1a095e491..0000000000
--- a/include/utils.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "utils.hxx" has moved to "bout/utils.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/utils.hxx"
diff --git a/include/vecops.hxx b/include/vecops.hxx
deleted file mode 100644
index 1773418077..0000000000
--- a/include/vecops.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "vecops.hxx" has moved to "bout/vecops.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/vecops.hxx"
diff --git a/include/vector2d.hxx b/include/vector2d.hxx
deleted file mode 100644
index 6746d3f163..0000000000
--- a/include/vector2d.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "vector2d.hxx" has moved to "bout/vector2d.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/vector2d.hxx"
diff --git a/include/vector3d.hxx b/include/vector3d.hxx
deleted file mode 100644
index 747b6a75dd..0000000000
--- a/include/vector3d.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "vector3d.hxx" has moved to "bout/vector3d.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/vector3d.hxx"
diff --git a/include/where.hxx b/include/where.hxx
deleted file mode 100644
index e5b2bd9d30..0000000000
--- a/include/where.hxx
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-// BOUT++ header shim
-#warning Header "where.hxx" has moved to "bout/where.hxx". Run `bin/bout-v5-header-upgrader.py` to fix
-#include "bout/where.hxx"