Changed source install manifest to allow us to pick from source distro or...

Changed source install manifest to allow us to pick from source distro or compiled (install/) output.

devtools/packaging/manifests/source/manifest.txt

-cmake_modules
-CMakeLists.txt
-docs-source
-docs
-examples
-libraries
-olla
-openmmapi
-platforms
-plugins
-serialization
-tests
-wrappers
+openmm/cmake_modules
+openmm/CMakeLists.txt
+openmm/docs-source
+install/docs
+openmm/examples
+openmm/libraries
+openmm/olla
+openmm/openmmapi
+openmm/platforms
+openmm/plugins
+openmm/serialization
+openmm/tests
+openmm/wrappers

devtools/packaging/scripts/source/build.sh

@@ -30,10 +30,10 @@ CMAKE_FLAGS+=" -DOPENMM_BUILD_RPMD_CUDA_LIB=OFF"
 CMAKE_FLAGS+=" -DOPENMM_BUILD_RPMD_OPENCL_LIB=OFF"
 
 # Set location for FFTW3
-PREFIX="$WORKSPACE/miniconda"
-CMAKE_FLAGS+=" -DFFTW_INCLUDES=$PREFIX/include"
-CMAKE_FLAGS+=" -DFFTW_LIBRARY=$PREFIX/lib/libfftw3f.so"
-CMAKE_FLAGS+=" -DFFTW_THREADS_LIBRARY=$PREFIX/lib/libfftw3f_threads.so"
+#PREFIX="$WORKSPACE/miniconda"
+#CMAKE_FLAGS+=" -DFFTW_INCLUDES=$PREFIX/include"
+#CMAKE_FLAGS+=" -DFFTW_LIBRARY=$PREFIX/lib/libfftw3f.so"
+#CMAKE_FLAGS+=" -DFFTW_THREADS_LIBRARY=$PREFIX/lib/libfftw3f_threads.so"
 
 # Build in subdirectory.
 if [ -e build ]; then

devtools/packaging/scripts/source/package.sh

@@ -19,7 +19,7 @@ rm -rf $PACKAGE_DIR
 mkdir $PACKAGE_DIR
 mkdir $PACKAGE_DIR/$PACKAGE_SUBDIR
 for filename in $( cat openmm/devtools/packaging/manifests/source/manifest.txt ); do
-   CMD="cp -r install/$filename $PACKAGE_DIR/$PACKAGE_SUBDIR"
+   CMD="cp -r $filename $PACKAGE_DIR/$PACKAGE_SUBDIR"
    echo $CMD
    `$CMD`
 done