1 files changed, 24 insertions, 21 deletions
diff --git a/biology/p5-Bio-Phylo/pkg-plist b/biology/p5-Bio-Phylo/pkg-plist
index 9a3cf20d0969..6c2f48982ef3 100644
--- a/biology/p5-Bio-Phylo/pkg-plist
+++ b/biology/p5-Bio-Phylo/pkg-plist
@@ -1,7 +1,4 @@
-%%SITE_PERL%%/Bio/._Phylo.pm
 %%SITE_PERL%%/Bio/Phylo.pm
-%%SITE_PERL%%/Bio/Phylo/Annotation.pm
-%%SITE_PERL%%/Bio/Phylo/Dictionary.pm
 %%SITE_PERL%%/Bio/Phylo/Forest.pm
 %%SITE_PERL%%/Bio/Phylo/Forest/DrawNode.pm
 %%SITE_PERL%%/Bio/Phylo/Forest/DrawTree.pm
@@ -25,23 +22,30 @@
 %%SITE_PERL%%/Bio/Phylo/Matrices/Datatype/Mixed.pm
 %%SITE_PERL%%/Bio/Phylo/Matrices/Datatype/Continuous.pm
 %%SITE_PERL%%/Bio/Phylo/Matrices/Datatype/Rna.pm
-%%SITE_PERL%%/Bio/Phylo/Mediators/NodeMediator.pm
 %%SITE_PERL%%/Bio/Phylo/Mediators/TaxaMediator.pm
-%%SITE_PERL%%/Bio/Phylo/Meta.pm
-%%SITE_PERL%%/Bio/Phylo/Meta/XMLLiteral.pm
+%%SITE_PERL%%/Bio/Phylo/NeXML/DOM/Document/Libxml.pm
+%%SITE_PERL%%/Bio/Phylo/NeXML/DOM/Document/Twig.pm
+%%SITE_PERL%%/Bio/Phylo/NeXML/DOM/Document/._Libxml.pm
+%%SITE_PERL%%/Bio/Phylo/NeXML/DOM/Document/._Twig.pm
+%%SITE_PERL%%/Bio/Phylo/NeXML/DOM/Element/._Twig.pm
+%%SITE_PERL%%/Bio/Phylo/NeXML/DOM/Element/Twig.pm
+%%SITE_PERL%%/Bio/Phylo/NeXML/DOM/Element/._Libxml.pm
+%%SITE_PERL%%/Bio/Phylo/NeXML/DOM/Element/Libxml.pm
+%%SITE_PERL%%/Bio/Phylo/NeXML/DOM/Document.pm
+%%SITE_PERL%%/Bio/Phylo/NeXML/DOM/Element.pm
+%%SITE_PERL%%/Bio/Phylo/NeXML/Meta/._XMLLiteral.pm
+%%SITE_PERL%%/Bio/Phylo/NeXML/Meta/XMLLiteral.pm
+%%SITE_PERL%%/Bio/Phylo/NeXML/._DOM.pm
+%%SITE_PERL%%/Bio/Phylo/NeXML/DOM.pm
+%%SITE_PERL%%/Bio/Phylo/NeXML/._Meta.pm
+%%SITE_PERL%%/Bio/Phylo/NeXML/Meta.pm
+%%SITE_PERL%%/Bio/Phylo/NeXML/Writable.pm
 %%SITE_PERL%%/Bio/Phylo/Parsers/Newick.pm
 %%SITE_PERL%%/Bio/Phylo/Parsers/Nexml.pm
 %%SITE_PERL%%/Bio/Phylo/Parsers/Nexus.pm
 %%SITE_PERL%%/Bio/Phylo/Parsers/Table.pm
 %%SITE_PERL%%/Bio/Phylo/Parsers/Taxlist.pm
 %%SITE_PERL%%/Bio/Phylo/Parsers/Tolweb.pm
-%%SITE_PERL%%/Bio/Phylo/PhyloWS.pm
-%%SITE_PERL%%/Bio/Phylo/PhyloWS/Resource/Description.pm
-%%SITE_PERL%%/Bio/Phylo/PhyloWS/Service/Tolweb.pm
-%%SITE_PERL%%/Bio/Phylo/PhyloWS/Service/Timetree.pm
-%%SITE_PERL%%/Bio/Phylo/PhyloWS/Client.pm
-%%SITE_PERL%%/Bio/Phylo/PhyloWS/Service.pm
-%%SITE_PERL%%/Bio/Phylo/PhyloWS/Resource.pm
 %%SITE_PERL%%/Bio/Phylo/Project.pm
 %%SITE_PERL%%/Bio/Phylo/Set.pm
 %%SITE_PERL%%/Bio/Phylo/Taxa.pm
@@ -55,18 +59,12 @@
 %%SITE_PERL%%/Bio/Phylo/Unparsers/Nexml.pm
 %%SITE_PERL%%/Bio/Phylo/Unparsers/Nexus.pm
 %%SITE_PERL%%/Bio/Phylo/Unparsers/Pagel.pm
-%%SITE_PERL%%/Bio/Phylo/Util/DOM/Document/libxml.pm
-%%SITE_PERL%%/Bio/Phylo/Util/DOM/Document/twig.pm
-%%SITE_PERL%%/Bio/Phylo/Util/DOM/Element/twig.pm
-%%SITE_PERL%%/Bio/Phylo/Util/DOM/Element/libxml.pm
-%%SITE_PERL%%/Bio/Phylo/Util/DOM/ElementI.pm
-%%SITE_PERL%%/Bio/Phylo/Util/DOM/DocumentI.pm
 %%SITE_PERL%%/Bio/Phylo/Util/Logger.pm
-%%SITE_PERL%%/Bio/Phylo/Util/DOM.pm
 %%SITE_PERL%%/Bio/Phylo/Util/CONSTANT.pm
 %%SITE_PERL%%/Bio/Phylo/Util/Exceptions.pm
 %%SITE_PERL%%/Bio/Phylo/Util/IDPool.pm
-%%SITE_PERL%%/Bio/Phylo/Util/XMLWritable.pm
+%%SITE_PERL%%/Bio/Phylo/Util/StackTrace.pm
+%%SITE_PERL%%/Bio/Phylo/Util/._StackTrace.pm
 %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio-Phylo/.packlist
 @dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio-Phylo
 @dirrm %%SITE_PERL%%/Bio/Phylo/Util/DOM/Document
@@ -80,6 +78,11 @@
 @dirrm %%SITE_PERL%%/Bio/Phylo/PhyloWS/Service
 @dirrm %%SITE_PERL%%/Bio/Phylo/PhyloWS
 @dirrm %%SITE_PERL%%/Bio/Phylo/Parsers
+@dirrm %%SITE_PERL%%/Bio/Phylo/NeXML/Meta
+@dirrm %%SITE_PERL%%/Bio/Phylo/NeXML/DOM/Element
+@dirrm %%SITE_PERL%%/Bio/Phylo/NeXML/DOM/Document
+@dirrm %%SITE_PERL%%/Bio/Phylo/NeXML/DOM
+@dirrm %%SITE_PERL%%/Bio/Phylo/NeXML
 @dirrm %%SITE_PERL%%/Bio/Phylo/Matrices/Datatype
 @dirrm %%SITE_PERL%%/Bio/Phylo/Matrices
 @dirrm %%SITE_PERL%%/Bio/Phylo/Mediators