1 files changed, 29 insertions, 24 deletions

diff --git a/biology/p5-Bio-Phylo/pkg-plist b/biology/p5-Bio-Phylo/pkg-plist
index 0ab74d1e453d..94b4195e3cf0 100644
--- a/biology/p5-Bio-Phylo/pkg-plist
+++ b/biology/p5-Bio-Phylo/pkg-plist
@@ -1,41 +1,41 @@
 %%SITE_PERL%%/Bio/Phylo.pm
 %%SITE_PERL%%/Bio/Phylo/EvolutionaryModels.pm
+%%SITE_PERL%%/Bio/Phylo/Factory.pm
 %%SITE_PERL%%/Bio/Phylo/Forest.pm
 %%SITE_PERL%%/Bio/Phylo/Forest/DrawNode.pm
 %%SITE_PERL%%/Bio/Phylo/Forest/DrawTree.pm
 %%SITE_PERL%%/Bio/Phylo/Forest/Node.pm
 %%SITE_PERL%%/Bio/Phylo/Forest/Tree.pm
 %%SITE_PERL%%/Bio/Phylo/Generator.pm
-%%SITE_PERL%%/Bio/Phylo/Identifiable.pm
 %%SITE_PERL%%/Bio/Phylo/IO.pm
-%%SITE_PERL%%/Bio/Phylo/Factory.pm
+%%SITE_PERL%%/Bio/Phylo/Identifiable.pm
 %%SITE_PERL%%/Bio/Phylo/Listable.pm
 %%SITE_PERL%%/Bio/Phylo/Manual.pod
 %%SITE_PERL%%/Bio/Phylo/Matrices.pm
-%%SITE_PERL%%/Bio/Phylo/Matrices/Characters.pm
 %%SITE_PERL%%/Bio/Phylo/Matrices/Character.pm
+%%SITE_PERL%%/Bio/Phylo/Matrices/Characters.pm
 %%SITE_PERL%%/Bio/Phylo/Matrices/Datatype.pm
-%%SITE_PERL%%/Bio/Phylo/Matrices/Datum.pm
-%%SITE_PERL%%/Bio/Phylo/Matrices/Matrix.pm
-%%SITE_PERL%%/Bio/Phylo/Matrices/TypeSafeData.pm
-%%SITE_PERL%%/Bio/Phylo/Matrices/Datatype/Protein.pm
-%%SITE_PERL%%/Bio/Phylo/Matrices/Datatype/Standard.pm
-%%SITE_PERL%%/Bio/Phylo/Matrices/Datatype/Restriction.pm
-%%SITE_PERL%%/Bio/Phylo/Matrices/Datatype/Dna.pm
+%%SITE_PERL%%/Bio/Phylo/Matrices/Datatype/Continuous.pm
 %%SITE_PERL%%/Bio/Phylo/Matrices/Datatype/Custom.pm
+%%SITE_PERL%%/Bio/Phylo/Matrices/Datatype/Dna.pm
 %%SITE_PERL%%/Bio/Phylo/Matrices/Datatype/Mixed.pm
-%%SITE_PERL%%/Bio/Phylo/Matrices/Datatype/Continuous.pm
+%%SITE_PERL%%/Bio/Phylo/Matrices/Datatype/Protein.pm
+%%SITE_PERL%%/Bio/Phylo/Matrices/Datatype/Restriction.pm
 %%SITE_PERL%%/Bio/Phylo/Matrices/Datatype/Rna.pm
+%%SITE_PERL%%/Bio/Phylo/Matrices/Datatype/Standard.pm
+%%SITE_PERL%%/Bio/Phylo/Matrices/Datum.pm
+%%SITE_PERL%%/Bio/Phylo/Matrices/Matrix.pm
+%%SITE_PERL%%/Bio/Phylo/Matrices/TypeSafeData.pm
 %%SITE_PERL%%/Bio/Phylo/Mediators/TaxaMediator.pm
+%%SITE_PERL%%/Bio/Phylo/NeXML/DOM.pm
+%%SITE_PERL%%/Bio/Phylo/NeXML/DOM/Document.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/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/DOM.pm
+%%SITE_PERL%%/Bio/Phylo/NeXML/DOM/Element/Libxml.pm
+%%SITE_PERL%%/Bio/Phylo/NeXML/DOM/Element/Twig.pm
 %%SITE_PERL%%/Bio/Phylo/NeXML/Meta.pm
+%%SITE_PERL%%/Bio/Phylo/NeXML/Meta/XMLLiteral.pm
 %%SITE_PERL%%/Bio/Phylo/NeXML/Writable.pm
 %%SITE_PERL%%/Bio/Phylo/Parsers/Abstract.pm
 %%SITE_PERL%%/Bio/Phylo/Parsers/Fasta.pm
@@ -51,19 +51,22 @@
 %%SITE_PERL%%/Bio/Phylo/Project.pm
 %%SITE_PERL%%/Bio/Phylo/Set.pm
 %%SITE_PERL%%/Bio/Phylo/Taxa.pm
-%%SITE_PERL%%/Bio/Phylo/Taxa/Taxon.pm
 %%SITE_PERL%%/Bio/Phylo/Taxa/TaxaLinker.pm
+%%SITE_PERL%%/Bio/Phylo/Taxa/Taxon.pm
 %%SITE_PERL%%/Bio/Phylo/Taxa/TaxonLinker.pm
 %%SITE_PERL%%/Bio/Phylo/Treedrawer.pm
+%%SITE_PERL%%/Bio/Phylo/Treedrawer/Abstract.pm
 %%SITE_PERL%%/Bio/Phylo/Treedrawer/Canvas.pm
-%%SITE_PERL%%/Bio/Phylo/Treedrawer/Pdf.pm
-%%SITE_PERL%%/Bio/Phylo/Treedrawer/Swf.pm
-%%SITE_PERL%%/Bio/Phylo/Treedrawer/Png.pm
 %%SITE_PERL%%/Bio/Phylo/Treedrawer/Gif.pm
 %%SITE_PERL%%/Bio/Phylo/Treedrawer/Jpeg.pm
-%%SITE_PERL%%/Bio/Phylo/Treedrawer/Abstract.pm
+%%SITE_PERL%%/Bio/Phylo/Treedrawer/Pdf.pm
+%%SITE_PERL%%/Bio/Phylo/Treedrawer/Png.pm
+%%SITE_PERL%%/Bio/Phylo/Treedrawer/Processing.pm
 %%SITE_PERL%%/Bio/Phylo/Treedrawer/Svg.pm
+%%SITE_PERL%%/Bio/Phylo/Treedrawer/Swf.pm
 %%SITE_PERL%%/Bio/Phylo/Unparsers/Abstract.pm
+%%SITE_PERL%%/Bio/Phylo/Unparsers/Fasta.pm
+%%SITE_PERL%%/Bio/Phylo/Unparsers/Json.pm
 %%SITE_PERL%%/Bio/Phylo/Unparsers/Mrp.pm
 %%SITE_PERL%%/Bio/Phylo/Unparsers/Newick.pm
 %%SITE_PERL%%/Bio/Phylo/Unparsers/Nexml.pm
@@ -71,10 +74,12 @@
 %%SITE_PERL%%/Bio/Phylo/Unparsers/Pagel.pm
 %%SITE_PERL%%/Bio/Phylo/Unparsers/Phylip.pm
 %%SITE_PERL%%/Bio/Phylo/Unparsers/Phyloxml.pm
-%%SITE_PERL%%/Bio/Phylo/Util/Logger.pm
 %%SITE_PERL%%/Bio/Phylo/Util/CONSTANT.pm
+%%SITE_PERL%%/Bio/Phylo/Util/Dependency.pm
 %%SITE_PERL%%/Bio/Phylo/Util/Exceptions.pm
 %%SITE_PERL%%/Bio/Phylo/Util/IDPool.pm
+%%SITE_PERL%%/Bio/Phylo/Util/Logger.pm
+%%SITE_PERL%%/Bio/Phylo/Util/OptionalInterface.pm
 %%SITE_PERL%%/Bio/Phylo/Util/StackTrace.pm
 %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio-Phylo/.packlist
 @dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio-Phylo
@@ -83,14 +88,14 @@
 @dirrm %%SITE_PERL%%/Bio/Phylo/Treedrawer
 @dirrm %%SITE_PERL%%/Bio/Phylo/Taxa
 @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/Meta
 @dirrm %%SITE_PERL%%/Bio/Phylo/NeXML
+@dirrm %%SITE_PERL%%/Bio/Phylo/Mediators
 @dirrm %%SITE_PERL%%/Bio/Phylo/Matrices/Datatype
 @dirrm %%SITE_PERL%%/Bio/Phylo/Matrices
-@dirrm %%SITE_PERL%%/Bio/Phylo/Mediators
 @dirrm %%SITE_PERL%%/Bio/Phylo/Forest
 @dirrm %%SITE_PERL%%/Bio/Phylo
 @dirrmtry %%SITE_PERL%%/Bio