1 files changed, 24 insertions, 21 deletions

diff --git a/biology/crux/pkg-plist b/biology/crux/pkg-plist
index 146a86412c1c..f95c872254d3 100644
--- a/biology/crux/pkg-plist
+++ b/biology/crux/pkg-plist
@@ -2,60 +2,63 @@
 bin/crux
 bin/redpoint
 bin/MrRogers
-%%PYTHON_SITELIBDIR%%/Crux/__init__.py
-%%PYTHON_SITELIBDIR%%/Crux/__init__.so
+%%PYTHON_SITELIBDIR%%/Crux/CTMatrix.so
 %%PYTHON_SITELIBDIR%%/Crux/Character.so
 %%PYTHON_SITELIBDIR%%/Crux/Config.py
 %%PYTHON_SITELIBDIR%%/Crux/Config.pyo
 %%PYTHON_SITELIBDIR%%/Crux/Copying.py
 %%PYTHON_SITELIBDIR%%/Crux/Copying.pyo
-%%PYTHON_SITELIBDIR%%/Crux/CTMatrix.so
+%%PYTHON_SITELIBDIR%%/Crux/DistMatrix/Nj.so
 %%PYTHON_SITELIBDIR%%/Crux/DistMatrix/__init__.py
 %%PYTHON_SITELIBDIR%%/Crux/DistMatrix/__init__.so
-%%PYTHON_SITELIBDIR%%/Crux/DistMatrix/Nj.so
 %%PYTHON_SITELIBDIR%%/Crux/Fasta.so
-%%PYTHON_SITELIBDIR%%/Crux/Mc3/__init__.py
-%%PYTHON_SITELIBDIR%%/Crux/Mc3/__init__.so
 %%PYTHON_SITELIBDIR%%/Crux/Mc3/Chain.so
 %%PYTHON_SITELIBDIR%%/Crux/Mc3/Post.so
+%%PYTHON_SITELIBDIR%%/Crux/Mc3/__init__.py
+%%PYTHON_SITELIBDIR%%/Crux/Mc3/__init__.so
 %%PYTHON_SITELIBDIR%%/Crux/Newick.so
 %%PYTHON_SITELIBDIR%%/Crux/Taxa.so
-%%PYTHON_SITELIBDIR%%/Crux/Tree/__init__.py
-%%PYTHON_SITELIBDIR%%/Crux/Tree/__init__.so
 %%PYTHON_SITELIBDIR%%/Crux/Tree/Bipart.so
 %%PYTHON_SITELIBDIR%%/Crux/Tree/Lik.so
 %%PYTHON_SITELIBDIR%%/Crux/Tree/Sumt.so
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/__init__.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Character.pxd
+%%PYTHON_SITELIBDIR%%/Crux/Tree/__init__.py
+%%PYTHON_SITELIBDIR%%/Crux/Tree/__init__.so
 %%PYTHON_SITELIBDIR%%/Crux/include/Crux/CTMatrix.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Cx.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/CxMath.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/CxMat.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/CxNewickLexer.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/CxRi.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/DistMatrix/__init__.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/DistMatrix/CxDistMatrixLexer.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Character.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Crux/CxMath.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Crux/CxMat.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Crux/CxNewickLexer.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Crux/CxRi.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Crux/Cx.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Crux/DistMatrix/CxDistMatrixLexer.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Crux/Tree/CxLik.pxd
 %%PYTHON_SITELIBDIR%%/Crux/include/Crux/DistMatrix/Nj.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/DistMatrix/__init__.pxd
 %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Fasta.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Mc3/__init__.pxd
 %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Mc3/Chain.pxd
 %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Mc3/Post.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Mc3/__init__.pxd
 %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Newick.pxd
 %%PYTHON_SITELIBDIR%%/Crux/include/Crux/SFMT/SFMT.pxd
 %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Taxa.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Tree/__init__.pxd
 %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Tree/Bipart.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Tree/CxLik.pxd
 %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Tree/Lik.pxd
 %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Tree/Sumt.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/libm.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Tree/__init__.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/__init__.pxd
 %%PYTHON_SITELIBDIR%%/Crux/include/Crux/libc.pxd
+%%PYTHON_SITELIBDIR%%/Crux/include/Crux/libm.pxd
 %%PYTHON_SITELIBDIR%%/Crux/include/Parsing.pxd
+%%PYTHON_SITELIBDIR%%/Crux/__init__.py
+%%PYTHON_SITELIBDIR%%/Crux/__init__.so
 %%PYTHON_SITELIBDIR%%/Parsing.so
 share/Crux/lib/libCx.so
 share/Crux/parsers/Fasta.log
 share/Crux/parsers/Fasta.pickle
 @dirrm %%PYTHON_SITELIBDIR%%/Crux/DistMatrix
+@dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Crux/DistMatrix
+@dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Crux/Tree
+@dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Crux
 @dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/DistMatrix
 @dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Mc3
 @dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/SFMT