diff --git a/cleanup.sh b/cleanup.sh
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index 000000000..1e5f2f7e8
--- /dev/null
+++ b/cleanup.sh
@@ -0,0 +1,9 @@
+#!/bin/sh
+# do some cleaning up to fix permissions and remove cruft
+
+find ./ -name \*.orig -print | xargs rm -v
+find ./ -name \*~ -print | xargs rm -v
+
+find ./ -name \*.cpp -print | xargs chmod -x
+find ./ -name \*.h -print | xargs chmod -x
+
diff --git a/lib/gpu/lal_eam_lj.cpp b/lib/gpu/lal_eam_lj.cpp
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diff --git a/lib/gpu/lal_eam_lj.h b/lib/gpu/lal_eam_lj.h
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diff --git a/lib/gpu/lal_eam_lj_ext.cpp b/lib/gpu/lal_eam_lj_ext.cpp
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diff --git a/src/DIPOLE/pair_lj_cut_dipole_cut.cpp b/src/DIPOLE/pair_lj_cut_dipole_cut.cpp
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diff --git a/src/DIPOLE/pair_lj_cut_dipole_cut.h b/src/DIPOLE/pair_lj_cut_dipole_cut.h
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diff --git a/src/DIPOLE/pair_lj_cut_dipole_long.cpp b/src/DIPOLE/pair_lj_cut_dipole_long.cpp
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diff --git a/src/DIPOLE/pair_lj_cut_dipole_long.h b/src/DIPOLE/pair_lj_cut_dipole_long.h
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diff --git a/src/DIPOLE/pair_lj_long_dipole_long.cpp b/src/DIPOLE/pair_lj_long_dipole_long.cpp
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diff --git a/src/DIPOLE/pair_lj_long_dipole_long.h b/src/DIPOLE/pair_lj_long_dipole_long.h
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diff --git a/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp b/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp
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diff --git a/src/GPU/pair_lj_cut_dipole_cut_gpu.h b/src/GPU/pair_lj_cut_dipole_cut_gpu.h
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diff --git a/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp b/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp
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diff --git a/src/GPU/pair_lj_sf_dipole_sf_gpu.h b/src/GPU/pair_lj_sf_dipole_sf_gpu.h
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diff --git a/src/KSPACE/pppm_stagger.cpp b/src/KSPACE/pppm_stagger.cpp
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diff --git a/src/KSPACE/pppm_stagger.h b/src/KSPACE/pppm_stagger.h
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diff --git a/src/USER-MISC/pair_lj_sf_dipole_sf.cpp b/src/USER-MISC/pair_lj_sf_dipole_sf.cpp
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diff --git a/src/USER-MISC/pair_lj_sf_dipole_sf.h b/src/USER-MISC/pair_lj_sf_dipole_sf.h
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diff --git a/src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp b/src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp
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diff --git a/src/USER-OMP/pair_lj_cut_dipole_cut_omp.h b/src/USER-OMP/pair_lj_cut_dipole_cut_omp.h
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diff --git a/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp b/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp
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diff --git a/src/USER-OMP/pair_lj_sf_dipole_sf_omp.h b/src/USER-OMP/pair_lj_sf_dipole_sf_omp.h
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diff --git a/src/atom_vec_ellipsoid.cpp b/src/atom_vec_ellipsoid.cpp
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diff --git a/tools/pymol_asphere/src/cartesian.cpp b/tools/pymol_asphere/src/cartesian.cpp
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diff --git a/tools/pymol_asphere/src/cartesian.h b/tools/pymol_asphere/src/cartesian.h
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diff --git a/tools/pymol_asphere/src/colors.cpp b/tools/pymol_asphere/src/colors.cpp
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diff --git a/tools/pymol_asphere/src/colors.h b/tools/pymol_asphere/src/colors.h
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diff --git a/tools/pymol_asphere/src/commandline.cpp b/tools/pymol_asphere/src/commandline.cpp
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diff --git a/tools/pymol_asphere/src/commandline.h b/tools/pymol_asphere/src/commandline.h
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diff --git a/tools/pymol_asphere/src/error.cpp b/tools/pymol_asphere/src/error.cpp
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diff --git a/tools/pymol_asphere/src/error.h b/tools/pymol_asphere/src/error.h
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diff --git a/tools/pymol_asphere/src/glsurface.cpp b/tools/pymol_asphere/src/glsurface.cpp
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diff --git a/tools/pymol_asphere/src/glsurface.h b/tools/pymol_asphere/src/glsurface.h
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diff --git a/tools/pymol_asphere/src/m_constants.h b/tools/pymol_asphere/src/m_constants.h
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diff --git a/tools/pymol_asphere/src/misc.cpp b/tools/pymol_asphere/src/misc.cpp
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diff --git a/tools/pymol_asphere/src/misc.h b/tools/pymol_asphere/src/misc.h
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diff --git a/tools/pymol_asphere/src/miscm.cpp b/tools/pymol_asphere/src/miscm.cpp
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diff --git a/tools/pymol_asphere/src/miscm.h b/tools/pymol_asphere/src/miscm.h
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diff --git a/tools/pymol_asphere/src/spherical.cpp b/tools/pymol_asphere/src/spherical.cpp
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diff --git a/tools/pymol_asphere/src/spherical.h b/tools/pymol_asphere/src/spherical.h
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diff --git a/tools/xmovie/resource.h b/tools/xmovie/resource.h
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diff --git a/tools/xmovie/xmovie.h b/tools/xmovie/xmovie.h
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