Cleanup plist

36 files changed, 0 insertions, 644 deletions

diff --git a/biology/artemis/pkg-plist b/biology/artemis/pkg-plist
index 175c8b5..491caaa 100644
--- a/biology/artemis/pkg-plist
+++ b/biology/artemis/pkg-plist
@@ -1778,34 +1778,3 @@ artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/util/WorkingGZIPInputStream.class
 artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/util/WorkingGZIPInputStream.java
 bin/act
 bin/art
-@dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/ibatis
-@dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/util
-@dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/sequence
-@dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot
-@dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/j2ssh
-@dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/io
-@dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor
-@dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/genebuilder/gff
-@dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/genebuilder/cv
-@dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/genebuilder
-@dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/filetree
-@dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/database
-@dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components
-@dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/chado
-@dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis
-@dirrm artemis-%%PORTVERSION%%/uk/ac/sanger
-@dirrm artemis-%%PORTVERSION%%/uk/ac
-@dirrm artemis-%%PORTVERSION%%/uk
-@dirrm artemis-%%PORTVERSION%%/type
-@dirrm artemis-%%PORTVERSION%%/seqdb
-@dirrm artemis-%%PORTVERSION%%/nsdb/NucFeaturePackage
-@dirrm artemis-%%PORTVERSION%%/nsdb/LocationPackage
-@dirrm artemis-%%PORTVERSION%%/nsdb/EmblPackage
-@dirrm artemis-%%PORTVERSION%%/nsdb
-@dirrm artemis-%%PORTVERSION%%/lib/j2ssh
-@dirrm artemis-%%PORTVERSION%%/lib/ibatis
-@dirrm artemis-%%PORTVERSION%%/lib
-@dirrm artemis-%%PORTVERSION%%/images
-@dirrm artemis-%%PORTVERSION%%/etc
-@dirrm artemis-%%PORTVERSION%%/artemis_sqlmap
-@dirrm artemis-%%PORTVERSION%%
diff --git a/biology/biococoa/pkg-plist b/biology/biococoa/pkg-plist
index 6d2080a..ccf74f7 100644
--- a/biology/biococoa/pkg-plist
+++ b/biology/biococoa/pkg-plist
@@ -63,8 +63,3 @@ GNUstep/Local/Library/Headers/BioCocoa
 GNUstep/Local/Library/Libraries/libBioCocoa.so
 GNUstep/Local/Library/Libraries/libBioCocoa.so.2
 GNUstep/Local/Library/Libraries/libBioCocoa.so.2.2.2
-@dirrmtry GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Resources
-@dirrmtry GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers
-@dirrmtry GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2
-@dirrmtry GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions
-@dirrmtry GNUstep/Local/Library/Frameworks/BioCocoa.framework
diff --git a/biology/crux/pkg-plist b/biology/crux/pkg-plist
index 2ec46cc..643a68f 100644
--- a/biology/crux/pkg-plist
+++ b/biology/crux/pkg-plist
@@ -54,19 +54,3 @@ lib/Crux/parsers/Fasta.pickle
 %%PYTHON_SITELIBDIR%%/Crux/__init__.py
 %%PYTHON_SITELIBDIR%%/Crux/__init__.so
 %%PYTHON_SITELIBDIR%%/Parsing.so
-@dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Tree
-@dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/SFMT
-@dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Mc3
-@dirrm %%PYTHON_SITELIBDIR%%/Crux/include/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
-@dirrm %%PYTHON_SITELIBDIR%%/Crux/include
-@dirrm %%PYTHON_SITELIBDIR%%/Crux/Tree
-@dirrm %%PYTHON_SITELIBDIR%%/Crux/Mc3
-@dirrm %%PYTHON_SITELIBDIR%%/Crux/DistMatrix
-@dirrm %%PYTHON_SITELIBDIR%%/Crux
-@dirrm lib/Crux/parsers
-@dirrm lib/Crux/lib
-@dirrm lib/Crux
diff --git a/biology/emboss/pkg-plist b/biology/emboss/pkg-plist
index 05d8dd5..c8161fe 100644
--- a/biology/emboss/pkg-plist
+++ b/biology/emboss/pkg-plist
@@ -2314,51 +2314,3 @@ lib/libnucleus.so.6.0.5
 %%PORTDOCS%%%%DOCSDIR%%/programs/text/wosstopic.txt
 %%PORTDOCS%%%%DOCSDIR%%/programs/text/xmlget.txt
 %%PORTDOCS%%%%DOCSDIR%%/programs/text/xmltext.txt
-@dirrm bin
-@dirrm include/ezlib
-@dirrm include/eplplot
-@dirrm include/epcre
-@dirrm include/eexpat
-@dirrm include
-@dirrm lib
-@dirrm %%DATADIR%%/acd
-@dirrm %%DATADIR%%/data/AAINDEX
-@dirrm %%DATADIR%%/data/CODONS
-@dirrm %%DATADIR%%/data/JASPAR_CNE
-@dirrm %%DATADIR%%/data/JASPAR_CORE
-@dirrm %%DATADIR%%/data/JASPAR_FAM
-@dirrm %%DATADIR%%/data/JASPAR_PHYLOFACTS
-@dirrm %%DATADIR%%/data/JASPAR_PBM
-@dirrm %%DATADIR%%/data/JASPAR_PBM_HLH
-@dirrm %%DATADIR%%/data/JASPAR_PBM_HOMEO
-@dirrm %%DATADIR%%/data/JASPAR_POLII
-@dirrm %%DATADIR%%/data/JASPAR_SPLICE
-@dirrm %%DATADIR%%/data/OBO
-@dirrm %%DATADIR%%/data/PRINTS
-@dirrm %%DATADIR%%/data/PROSITE
-@dirrm %%DATADIR%%/data/REBASE
-@dirrm %%DATADIR%%/data/TAXONOMY
-@dirrm %%DATADIR%%/data
-@dirrm %%DATADIR%%/index
-@dirrm %%DATADIR%%/jemboss/images
-@dirrm %%DATADIR%%/jemboss/lib/axis
-@dirrm %%DATADIR%%/jemboss/lib
-@dirrm %%DATADIR%%/jemboss/resources
-@dirrm %%DATADIR%%/jemboss/utils
-@dirrm %%DATADIR%%/jemboss
-@dirrm %%DATADIR%%/test/data
-@dirrm %%DATADIR%%/test/embl
-@dirrm %%DATADIR%%/test/genbank
-@dirrm %%DATADIR%%/test/pir
-@dirrm %%DATADIR%%/test/swiss
-@dirrm %%DATADIR%%/test/swnew
-@dirrm %%DATADIR%%/test/testdb
-@dirrm %%DATADIR%%/test
-@dirrmtry %%DATADIR%%
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/manuals
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/programs/html
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/programs/text
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/programs
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/tutorials
-%%PORTDOCS%%@dirrm %%DOCSDIR%%
-@dirrmtry share
diff --git a/biology/fasta3/pkg-plist b/biology/fasta3/pkg-plist
index 714dfe3..92323bb 100644
--- a/biology/fasta3/pkg-plist
+++ b/biology/fasta3/pkg-plist
@@ -118,6 +118,3 @@ man/man1/tfasty35.1.gz
 %%DATADIR%%/pam250.mat
 %%DATADIR%%/rna.mat
 %%DATADIR%%/vtml160.mat
-@dirrm %%DATADIR%%
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%
-%%PORTDOCS%%@dirrm %%DOCSDIR%%
diff --git a/biology/fastdnaml/pkg-plist b/biology/fastdnaml/pkg-plist
index 4ec8465..23baeaa 100644
--- a/biology/fastdnaml/pkg-plist
+++ b/biology/fastdnaml/pkg-plist
@@ -32,4 +32,3 @@ bin/fastdnaml/usertree
 bin/fastdnaml/usertrees
 bin/fastdnaml/weights
 bin/fastdnaml/weights_categories
-@dirrm bin/fastdnaml
diff --git a/biology/garlic/pkg-plist b/biology/garlic/pkg-plist
index f7c1665..9e2c6b9 100644
--- a/biology/garlic/pkg-plist
+++ b/biology/garlic/pkg-plist
@@ -1,7 +1,6 @@
 bin/garlic
 share/garlic/.garlicrc
 share/garlic/residues.pdb
-@dirrm share/garlic
 %%PORTDOCS%%%%DOCSDIR%%/README
 %%PORTDOCS%%%%DOCSDIR%%/ascorbic_acid1.jpg
 %%PORTDOCS%%%%DOCSDIR%%/ascorbic_acid2.jpg
@@ -258,30 +257,6 @@ share/garlic/residues.pdb
 %%PORTDOCS%%%%DOCSDIR%%/whatis/favicon.ico
 %%PORTDOCS%%%%DOCSDIR%%/whatis/garlic.gif
 %%PORTDOCS%%%%DOCSDIR%%/whatis/index.html
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/whatis
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/tutorial
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/techinfo
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/support
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/scripts
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/refcard
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/precompiled_packages
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/options
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/mouse/.xvpics
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/mouse
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/license
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/install
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/gallery
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/features
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/download
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/data
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/cookbook
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/controls
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/config
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/competition
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/commands
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/changes
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/bugfixes
-%%PORTDOCS%%@dirrm %%DOCSDIR%%
 %%PORTDOCS%%%%EXAMPLESDIR%%/adrenaline.pdb
 %%PORTDOCS%%%%EXAMPLESDIR%%/22porins.script
 %%PORTDOCS%%%%EXAMPLESDIR%%/backup-hyd.script
@@ -325,4 +300,3 @@ share/garlic/residues.pdb
 %%PORTDOCS%%%%EXAMPLESDIR%%/trp.pdb
 %%PORTDOCS%%%%EXAMPLESDIR%%/two-positive.script
 %%PORTDOCS%%%%EXAMPLESDIR%%/water.pdb
-%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%
diff --git a/biology/hmmer/pkg-plist b/biology/hmmer/pkg-plist
index 9b66c29..b96ba0d 100644
--- a/biology/hmmer/pkg-plist
+++ b/biology/hmmer/pkg-plist
@@ -43,5 +43,3 @@ man/man1/phmmer.1.gz
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/globins4.out
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.h3m
-%%PORTDOCS%%@dirrm %%DOCSDIR%%
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%
diff --git a/biology/iolib/pkg-plist b/biology/iolib/pkg-plist
index cb1cee9..2ed7e25 100644
--- a/biology/iolib/pkg-plist
+++ b/biology/iolib/pkg-plist
@@ -110,4 +110,3 @@ man/man3/write_reading.3.gz
 man/man3/write_scf.3.gz
 man/man3/write_scf_header.3.gz
 man/man4/Read.4.gz
-@dirrmtry include/io_lib
diff --git a/biology/jalview/pkg-plist b/biology/jalview/pkg-plist
index bec3391..763d294 100644
--- a/biology/jalview/pkg-plist
+++ b/biology/jalview/pkg-plist
@@ -14,4 +14,3 @@ bin/jalview
 %%DATADIR%%/castor-0.9.6-xml.jar
 %%DATADIR%%/axis.jar
 %%DATADIR%%/xml-apis.jar
-@dirrm %%DATADIR%%
diff --git a/biology/libsbml/pkg-plist b/biology/libsbml/pkg-plist
index 106b9d1..3a811ca 100644
--- a/biology/libsbml/pkg-plist
+++ b/biology/libsbml/pkg-plist
@@ -492,37 +492,3 @@ lib/libsbml.so.5.10.2
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-3/twoalgebraicrules.xml
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-3/twodimensional.xml
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/xslt/layout/layout2svg.xsl
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/xslt/layout
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/xslt
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/sample-models/from-spec/level-3
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/sample-models/from-spec/level-2
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/sample-models/from-spec
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/sample-models
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/ruby/layout
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/ruby
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/r
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/python/layout
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/python
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/perl/layout
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/perl
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/layout
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/java/layout
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/java
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/csharp/layout
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/csharp
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/c++/layout
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/c++
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/c
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%
-%%PYTHON%%@dirrm %%PYTHON_SITELIBDIR%%/libsbml
-@dirrm include/sbml/xml
-@dirrm include/sbml/validator
-@dirrm include/sbml/util
-@dirrm include/sbml/units
-@dirrm include/sbml/math
-@dirrm include/sbml/extension
-@dirrm include/sbml/conversion
-@dirrm include/sbml/compress
-@dirrm include/sbml/common
-@dirrm include/sbml/annotation
-@dirrm include/sbml
diff --git a/biology/mafft/pkg-plist b/biology/mafft/pkg-plist
index 06086ea..3bb0b78 100644
--- a/biology/mafft/pkg-plist
+++ b/biology/mafft/pkg-plist
@@ -66,6 +66,3 @@ man/man1/mafft.1.gz
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/samplerna
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/samplerna.qinsi
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/samplerna.xinsi
-@dirrmtry libexec/mafft
-%%PORTDOCS%%@dirrmtry %%DOCSDIR%%
-%%PORTEXAMPLES%%@dirrmtry %%EXAMPLESDIR%%
diff --git a/biology/mopac/pkg-plist b/biology/mopac/pkg-plist
index 5471c97..baebca1 100644
--- a/biology/mopac/pkg-plist
+++ b/biology/mopac/pkg-plist
@@ -6,4 +6,3 @@ lib/libmopac7.so.0
 lib/libmopac7.so.0.0.0
 libdata/pkgconfig/libmopac7.pc
 libexec/mopac7
-@dirrm include/mopac7
diff --git a/biology/mummer/pkg-plist b/biology/mummer/pkg-plist
index d569fa3..ea64212 100644
--- a/biology/mummer/pkg-plist
+++ b/biology/mummer/pkg-plist
@@ -23,4 +23,3 @@ bin/show-tiling
 %%PORTDOCS%%%%DOCSDIR%%/INSTALL
 %%PORTDOCS%%%%DOCSDIR%%/LICENSE
 %%PORTDOCS%%%%DOCSDIR%%/README
-%%PORTDOCS%%@dirrm %%DOCSDIR%%
diff --git a/biology/ncbi-toolkit/pkg-plist b/biology/ncbi-toolkit/pkg-plist
index 63be592..efd3cb7 100644
--- a/biology/ncbi-toolkit/pkg-plist
+++ b/biology/ncbi-toolkit/pkg-plist
@@ -811,12 +811,3 @@ man/man1/vecscreen.1.gz
 %%DATADIR%%/sgmlbb.ent
 %%DATADIR%%/taxlist.txt
 %%DATADIR%%/validrules.prt
-@dirrmtry %%DATADIR%%
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/seq_install
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/images
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/fa2htgs
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/blast
-%%PORTDOCS%%@dirrm %%DOCSDIR%%
-@dirrm lib/ncbi
-@dirrm include/ncbi/connect
-@dirrm include/ncbi
diff --git a/biology/p5-AcePerl/pkg-plist b/biology/p5-AcePerl/pkg-plist
index 3a7cbd2..3ac0b3a 100644
--- a/biology/p5-AcePerl/pkg-plist
+++ b/biology/p5-AcePerl/pkg-plist
@@ -144,16 +144,3 @@ bin/ace.pl
 %%PERL5_MAN3%%/Ace::Sequence::Multi.3.gz
 %%PERL5_MAN3%%/Ace::Sequence::Transcript.3.gz
 man/man1/ace.pl.1.gz
-@dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Sequence/Feature
-@dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Sequence
-@dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/RPC
-@dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object
-@dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Freesubs
-@dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace
-@dirrm %%SITE_PERL%%/%%PERL_ARCH%%/GFF
-@dirrm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Sequence
-@dirrm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Object
-@dirrm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph
-@dirrm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics
-@dirrm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Browser
-@dirrm %%SITE_PERL%%/%%PERL_ARCH%%/Ace
diff --git a/biology/p5-Bio-ASN1-EntrezGene/pkg-plist b/biology/p5-Bio-ASN1-EntrezGene/pkg-plist
index 085ac8e..4014f2c 100644
--- a/biology/p5-Bio-ASN1-EntrezGene/pkg-plist
+++ b/biology/p5-Bio-ASN1-EntrezGene/pkg-plist
@@ -7,10 +7,3 @@
 %%PERL5_MAN3%%/Bio::ASN1::EntrezGene::Indexer.3.gz
 %%PERL5_MAN3%%/Bio::ASN1::Sequence.3.gz
 %%PERL5_MAN3%%/Bio::ASN1::Sequence::Indexer.3.gz
-@dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/ASN1/EntrezGene
-@dirrmtry %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/ASN1
-@dirrmtry %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio
-@dirrmtry %%SITE_PERL%%/Bio/ASN1/EntrezGene
-@dirrmtry %%SITE_PERL%%/Bio/ASN1/Sequence
-@dirrmtry %%SITE_PERL%%/Bio/ASN1
-@dirrmtry %%SITE_PERL%%/Bio
diff --git a/biology/p5-Bio-Das-Lite/pkg-plist b/biology/p5-Bio-Das-Lite/pkg-plist
index 988f857..d3c9e87 100644
--- a/biology/p5-Bio-Das-Lite/pkg-plist
+++ b/biology/p5-Bio-Das-Lite/pkg-plist
@@ -1,4 +1,2 @@
 %%SITE_PERL%%/Bio/Das/Lite.pm
 %%PERL5_MAN3%%/Bio::Das::Lite.3.gz
-@dirrmtry %%SITE_PERL%%/Bio/Das
-@dirrmtry %%SITE_PERL%%/Bio
diff --git a/biology/p5-Bio-Das/pkg-plist b/biology/p5-Bio-Das/pkg-plist
index 285c653..a67510c 100644
--- a/biology/p5-Bio-Das/pkg-plist
+++ b/biology/p5-Bio-Das/pkg-plist
@@ -51,10 +51,3 @@
 %%PERL5_MAN3%%/Bio::Das::Type.3.gz
 %%PERL5_MAN3%%/Bio::Das::TypeHandler.3.gz
 %%PERL5_MAN3%%/Bio::Das::Util.3.gz
-@dirrmtry %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/Das
-@dirrmtry %%SITE_PERL%%/Bio/Das/Request
-@dirrmtry %%SITE_PERL%%/Bio/Das/HTTP
-@dirrmtry %%SITE_PERL%%/Bio/Das/AGPServer/SQLStorage/MySQL
-@dirrmtry %%SITE_PERL%%/Bio/Das/AGPServer/SQLStorage/CSV
-@dirrmtry %%SITE_PERL%%/Bio/Das/AGPServer/SQLStorage
-@dirrmtry %%SITE_PERL%%/Bio/Das/AGPServer
diff --git a/biology/p5-Bio-GFF3/pkg-plist b/biology/p5-Bio-GFF3/pkg-plist
index bdea405..b8448e9 100644
--- a/biology/p5-Bio-GFF3/pkg-plist
+++ b/biology/p5-Bio-GFF3/pkg-plist
@@ -11,10 +11,3 @@ bin/gff3_from_fasta
 %%PERL5_MAN3%%/Bio::GFF3::Transform::FromFasta.3.gz
 %%PERL5_MAN3%%/Bio::GFF3::Transform::SyncDirectives.3.gz
 man/man1/gff3_from_fasta.1.gz
-@dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/GFF3
-@dirrmtry %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio
-@dirrm %%SITE_PERL%%/Bio/GFF3/Transform
-@dirrm %%SITE_PERL%%/Bio/GFF3/LowLevel/Parser
-@dirrm %%SITE_PERL%%/Bio/GFF3/LowLevel
-@dirrm %%SITE_PERL%%/Bio/GFF3
-@dirrmtry %%SITE_PERL%%/Bio
diff --git a/biology/p5-Bio-Glite/pkg-plist b/biology/p5-Bio-Glite/pkg-plist
index 861f941..e3d6145 100644
--- a/biology/p5-Bio-Glite/pkg-plist
+++ b/biology/p5-Bio-Glite/pkg-plist
@@ -1,6 +1,3 @@
 %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/Glite/.packlist
 %%SITE_PERL%%/Bio/Glite.pm
 %%PERL5_MAN3%%/Bio::Glite.3.gz
-@dirrmtry %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/Glite
-@dirrmtry %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio
-@dirrmtry %%SITE_PERL%%/Bio
diff --git a/biology/p5-Bio-Graphics/pkg-plist b/biology/p5-Bio-Graphics/pkg-plist
index 4ef8598..b97abc1 100644
--- a/biology/p5-Bio-Graphics/pkg-plist
+++ b/biology/p5-Bio-Graphics/pkg-plist
@@ -216,7 +216,3 @@ man/man1/contig_draw.pl.1.gz
 man/man1/feature_draw.pl.1.gz
 man/man1/frend.pl.1.gz
 man/man1/search_overview.pl.1.gz
-@dirrmtry %%SITE_PERL%%/Bio/Graphics/FeatureFile
-@dirrmtry %%SITE_PERL%%/Bio/Graphics/Glyph
-@dirrmtry %%SITE_PERL%%/Bio/Graphics/Wiggle
-@dirrmtry %%SITE_PERL%%/Bio/Graphics
diff --git a/biology/p5-Bio-MAGETAB/pkg-plist b/biology/p5-Bio-MAGETAB/pkg-plist
index e902096..dc6cee7 100644
--- a/biology/p5-Bio-MAGETAB/pkg-plist
+++ b/biology/p5-Bio-MAGETAB/pkg-plist
@@ -117,10 +117,3 @@ bin/unload_magetab_namespace.pl
 %%PERL5_MAN3%%/Bio::MAGETAB::Util::Writer::IDF.3.gz
 %%PERL5_MAN3%%/Bio::MAGETAB::Util::Writer::SDRF.3.gz
 %%PERL5_MAN3%%/Bio::MAGETAB::Util::Writer::Tabfile.3.gz
-@dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/MAGETAB
-@dirrmtry %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio
-@dirrm %%SITE_PERL%%/Bio/MAGETAB/Util/Reader
-@dirrm %%SITE_PERL%%/Bio/MAGETAB/Util/Writer
-@dirrm %%SITE_PERL%%/Bio/MAGETAB/Util
-@dirrm %%SITE_PERL%%/Bio/MAGETAB
-@dirrmtry %%SITE_PERL%%/Bio
diff --git a/biology/p5-Bio-NEXUS/pkg-plist b/biology/p5-Bio-NEXUS/pkg-plist
index ce2f755..76b687a 100644
--- a/biology/p5-Bio-NEXUS/pkg-plist
+++ b/biology/p5-Bio-NEXUS/pkg-plist
@@ -61,9 +61,3 @@ bin/nextool.pl
 man/man1/nex2text_tree.pl.1.gz
 man/man1/nexplot.pl.1.gz
 man/man1/nextool.pl.1.gz
-@dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/NEXUS
-@dirrmtry %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio
-@dirrm %%SITE_PERL%%/Bio/NEXUS/Util
-@dirrm %%SITE_PERL%%/Bio/NEXUS/Tools
-@dirrm %%SITE_PERL%%/Bio/NEXUS
-@dirrmtry %%SITE_PERL%%/Bio
diff --git a/biology/p5-Bio-Phylo/pkg-plist b/biology/p5-Bio-Phylo/pkg-plist
index 7653911..c353f68 100644
--- a/biology/p5-Bio-Phylo/pkg-plist
+++ b/biology/p5-Bio-Phylo/pkg-plist
@@ -239,28 +239,3 @@
 %%PERL5_MAN3%%/Bio::Phylo::Util::OptionalInterface.3.gz
 %%PERL5_MAN3%%/Bio::Phylo::Util::StackTrace.3.gz
 %%PERL5_MAN3%%/Bio::PhyloRole.3.gz
-@dirrm %%SITE_PERL%%/Bio/Phylo/Util/CONSTANT
-@dirrm %%SITE_PERL%%/Bio/Phylo/Util
-@dirrm %%SITE_PERL%%/Bio/Phylo/Unparsers
-@dirrm %%SITE_PERL%%/Bio/Phylo/Treedrawer
-@dirrm %%SITE_PERL%%/Bio/Phylo/Taxa
-@dirrm %%SITE_PERL%%/Bio/Phylo/PhyloWS/Service
-@dirrm %%SITE_PERL%%/Bio/Phylo/PhyloWS/Resource
-@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/Models/Substitution/Dna
-@dirrm %%SITE_PERL%%/Bio/Phylo/Models/Substitution
-@dirrm %%SITE_PERL%%/Bio/Phylo/Models
-@dirrm %%SITE_PERL%%/Bio/Phylo/Mediators
-@dirrm %%SITE_PERL%%/Bio/Phylo/Matrices/Datatype
-@dirrm %%SITE_PERL%%/Bio/Phylo/Matrices
-@dirrm %%SITE_PERL%%/Bio/Phylo/Forest
-@dirrm %%SITE_PERL%%/Bio/Phylo
-@dirrmtry %%SITE_PERL%%/Bio
-@dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/Phylo
-@dirrmtry %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio
diff --git a/biology/p5-Bio-SCF/pkg-plist b/biology/p5-Bio-SCF/pkg-plist
index 1cd5f3a..34287ac 100644
--- a/biology/p5-Bio-SCF/pkg-plist
+++ b/biology/p5-Bio-SCF/pkg-plist
@@ -3,7 +3,3 @@
 %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/SCF/SCF.so
 %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/SCF/.packlist
 %%PERL5_MAN3%%/Bio::SCF.3.gz
-@dirrmtry %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/SCF
-@dirrmtry %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio
-@dirrmtry %%SITE_PERL%%/%%PERL_ARCH%%/Bio/SCF
-@dirrmtry %%SITE_PERL%%/%%PERL_ARCH%%/Bio
diff --git a/biology/p5-bioperl-run/pkg-plist b/biology/p5-bioperl-run/pkg-plist
index 03c024d..75240a9 100644
--- a/biology/p5-bioperl-run/pkg-plist
+++ b/biology/p5-bioperl-run/pkg-plist
@@ -261,25 +261,3 @@ bin/bp_run_protdist
 %%PORTDOCS%%%%DOCSDIR%%/Changes
 %%PORTDOCS%%%%DOCSDIR%%/INSTALL.PROGRAMS
 %%PORTDOCS%%%%DOCSDIR%%/README
-@dirrmtry %%SITE_PERL%%/Bio/DB/ESoap
-@dirrmtry %%SITE_PERL%%/Bio/DB/SoapEUtilities/FetchAdaptor
-@dirrmtry %%SITE_PERL%%/Bio/DB/SoapEUtilities
-@dirrmtry %%SITE_PERL%%/Bio/Installer
-@dirrmtry %%SITE_PERL%%/Bio/Tools/Run/Alignment
-@dirrmtry %%SITE_PERL%%/Bio/Tools/Run/Analysis
-@dirrmtry %%SITE_PERL%%/Bio/Tools/Run/AnalysisFactory
-@dirrmtry %%SITE_PERL%%/Bio/Tools/Run/BEDTools
-@dirrmtry %%SITE_PERL%%/Bio/Tools/Run/BWA
-@dirrmtry %%SITE_PERL%%/Bio/Tools/Run/BlastPlus
-@dirrmtry %%SITE_PERL%%/Bio/Tools/Run/Bowtie
-@dirrmtry %%SITE_PERL%%/Bio/Tools/Run/Maq
-@dirrmtry %%SITE_PERL%%/Bio/Tools/Run/Phylo/Hyphy
-@dirrmtry %%SITE_PERL%%/Bio/Tools/Run/Phylo/Molphy
-@dirrmtry %%SITE_PERL%%/Bio/Tools/Run/Phylo/Njtree
-@dirrmtry %%SITE_PERL%%/Bio/Tools/Run/Phylo/PAML
-@dirrmtry %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phast
-@dirrmtry %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip
-@dirrmtry %%SITE_PERL%%/Bio/Tools/Run/Phylo
-@dirrmtry %%SITE_PERL%%/Bio/Tools/Run/Samtools
-@dirrmtry %%SITE_PERL%%/Bio/Tools/Run/StandAloneBlastPlus
-%%PORTDOCS%%@dirrmtry %%DOCSDIR%%
diff --git a/biology/p5-bioperl/pkg-plist b/biology/p5-bioperl/pkg-plist
index 2fb88f2..1203eb0 100644
--- a/biology/p5-bioperl/pkg-plist
+++ b/biology/p5-bioperl/pkg-plist
@@ -1937,159 +1937,3 @@ man/man1/bp_unflatten_seq.pl.1.gz
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/seq_pattern.pl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/standaloneblast.pl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/tree/paup2phylip.pl
-@dirrm %%SITE_PERL%%/Bio/Align
-@dirrm %%SITE_PERL%%/Bio/AlignIO/Handler
-@dirrm %%SITE_PERL%%/Bio/AlignIO
-@dirrm %%SITE_PERL%%/Bio/Annotation
-@dirrm %%SITE_PERL%%/Bio/Assembly/IO
-@dirrm %%SITE_PERL%%/Bio/Assembly/Tools
-@dirrm %%SITE_PERL%%/Bio/Assembly
-@dirrm %%SITE_PERL%%/Bio/Cluster
-@dirrm %%SITE_PERL%%/Bio/ClusterIO
-@dirrm %%SITE_PERL%%/Bio/CodonUsage
-@dirrm %%SITE_PERL%%/Bio/Coordinate/Result
-@dirrm %%SITE_PERL%%/Bio/Coordinate
-@dirrm %%SITE_PERL%%/Bio/DB/Expression
-@dirrm %%SITE_PERL%%/Bio/DB/Flat/BDB
-@dirrm %%SITE_PERL%%/Bio/DB/Flat
-@dirrm %%SITE_PERL%%/Bio/DB/GFF/Adaptor/berkeleydb
-@dirrm %%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi
-@dirrm %%SITE_PERL%%/Bio/DB/GFF/Adaptor/memory
-@dirrm %%SITE_PERL%%/Bio/DB/GFF/Adaptor
-@dirrm %%SITE_PERL%%/Bio/DB/GFF/Aggregator
-@dirrm %%SITE_PERL%%/Bio/DB/GFF/Util
-@dirrm %%SITE_PERL%%/Bio/DB/GFF
-@dirrm %%SITE_PERL%%/Bio/DB/HIV
-@dirrm %%SITE_PERL%%/Bio/DB/Query
-@dirrm %%SITE_PERL%%/Bio/DB/SeqFeature/Store/DBI
-@dirrm %%SITE_PERL%%/Bio/DB/SeqFeature/Store
-@dirrm %%SITE_PERL%%/Bio/DB/SeqFeature
-@dirrm %%SITE_PERL%%/Bio/DB/SeqVersion
-@dirrm %%SITE_PERL%%/Bio/DB/TFBS
-@dirrm %%SITE_PERL%%/Bio/DB/Taxonomy
-@dirrm %%SITE_PERL%%/Bio/DB
-@dirrm %%SITE_PERL%%/Bio/Das
-@dirrm %%SITE_PERL%%/Bio/Draw
-@dirrm %%SITE_PERL%%/Bio/Event
-@dirrm %%SITE_PERL%%/Bio/Factory
-@dirrm %%SITE_PERL%%/Bio/Index
-@dirrm %%SITE_PERL%%/Bio/LiveSeq/IO
-@dirrm %%SITE_PERL%%/Bio/LiveSeq
-@dirrm %%SITE_PERL%%/Bio/Location
-@dirrm %%SITE_PERL%%/Bio/Map
-@dirrm %%SITE_PERL%%/Bio/MapIO
-@dirrm %%SITE_PERL%%/Bio/Matrix/IO
-@dirrm %%SITE_PERL%%/Bio/Matrix/PSM/IO
-@dirrm %%SITE_PERL%%/Bio/Matrix/PSM
-@dirrm %%SITE_PERL%%/Bio/Matrix
-@dirrm %%SITE_PERL%%/Bio/MolEvol
-@dirrm %%SITE_PERL%%/Bio/Nexml
-@dirrm %%SITE_PERL%%/Bio/Ontology/SimpleGOEngine
-@dirrm %%SITE_PERL%%/Bio/Ontology
-@dirrm %%SITE_PERL%%/Bio/OntologyIO/Handlers
-@dirrm %%SITE_PERL%%/Bio/OntologyIO
-@dirrm %%SITE_PERL%%/Bio/Phenotype/MeSH
-@dirrm %%SITE_PERL%%/Bio/Phenotype/OMIM
-@dirrm %%SITE_PERL%%/Bio/Phenotype
-@dirrm %%SITE_PERL%%/Bio/PhyloNetwork
-@dirrm %%SITE_PERL%%/Bio/PopGen/IO
-@dirrm %%SITE_PERL%%/Bio/PopGen/Simulation
-@dirrm %%SITE_PERL%%/Bio/PopGen
-@dirrm %%SITE_PERL%%/Bio/Restriction/Enzyme
-@dirrm %%SITE_PERL%%/Bio/Restriction/IO
-@dirrm %%SITE_PERL%%/Bio/Restriction
-@dirrm %%SITE_PERL%%/Bio/Root
-@dirrm %%SITE_PERL%%/Bio/Search/HSP
-@dirrm %%SITE_PERL%%/Bio/Search/Hit
-@dirrm %%SITE_PERL%%/Bio/Search/Iteration
-@dirrm %%SITE_PERL%%/Bio/Search/Result
-@dirrm %%SITE_PERL%%/Bio/Search/Tiling
-@dirrm %%SITE_PERL%%/Bio/Search
-@dirrm %%SITE_PERL%%/Bio/SearchIO/Writer
-@dirrm %%SITE_PERL%%/Bio/SearchIO/XML
-@dirrm %%SITE_PERL%%/Bio/SearchIO
-@dirrm %%SITE_PERL%%/Bio/Seq/Meta
-@dirrm %%SITE_PERL%%/Bio/Seq
-@dirrm %%SITE_PERL%%/Bio/SeqEvolution
-@dirrm %%SITE_PERL%%/Bio/SeqFeature/Gene
-@dirrm %%SITE_PERL%%/Bio/SeqFeature/SiRNA
-@dirrm %%SITE_PERL%%/Bio/SeqFeature/Tools
-@dirrm %%SITE_PERL%%/Bio/SeqFeature
-@dirrm %%SITE_PERL%%/Bio/SeqIO/Handler
-@dirrm %%SITE_PERL%%/Bio/SeqIO/game
-@dirrm %%SITE_PERL%%/Bio/SeqIO/tinyseq
-@dirrm %%SITE_PERL%%/Bio/SeqIO
-@dirrm %%SITE_PERL%%/Bio/Structure/IO
-@dirrm %%SITE_PERL%%/Bio/Structure/SecStr/DSSP
-@dirrm %%SITE_PERL%%/Bio/Structure/SecStr/STRIDE
-@dirrm %%SITE_PERL%%/Bio/Structure/SecStr
-@dirrm %%SITE_PERL%%/Bio/Structure
-@dirrm %%SITE_PERL%%/Bio/Symbol
-@dirrm %%SITE_PERL%%/Bio/Taxonomy
-@dirrm %%SITE_PERL%%/Bio/Tools/Alignment
-@dirrm %%SITE_PERL%%/Bio/Tools/Analysis/DNA
-@dirrm %%SITE_PERL%%/Bio/Tools/Analysis/Protein
-@dirrm %%SITE_PERL%%/Bio/Tools/Analysis
-@dirrm %%SITE_PERL%%/Bio/Tools/EMBOSS
-@dirrm %%SITE_PERL%%/Bio/Tools/HMMER
-@dirrm %%SITE_PERL%%/Bio/Tools/Phylo/Molphy
-@dirrm %%SITE_PERL%%/Bio/Tools/Phylo/PAML
-@dirrm %%SITE_PERL%%/Bio/Tools/Phylo/Phylip
-@dirrm %%SITE_PERL%%/Bio/Tools/Phylo
-@dirrm %%SITE_PERL%%/Bio/Tools/Prediction
-@dirrm %%SITE_PERL%%/Bio/Tools/Primer/Assessor
-@dirrm %%SITE_PERL%%/Bio/Tools/Primer
-@dirrm %%SITE_PERL%%/Bio/Tools/Run/WrapperBase
-@dirrm %%SITE_PERL%%/Bio/Tools/Run
-@dirrm %%SITE_PERL%%/Bio/Tools/SeqPattern
-@dirrm %%SITE_PERL%%/Bio/Tools/SiRNA/Ruleset
-@dirrm %%SITE_PERL%%/Bio/Tools/SiRNA
-@dirrm %%SITE_PERL%%/Bio/Tools/Signalp
-@dirrm %%SITE_PERL%%/Bio/Tools/Sim4
-@dirrm %%SITE_PERL%%/Bio/Tools/Spidey
-@dirrm %%SITE_PERL%%/Bio/Tools
-@dirrm %%SITE_PERL%%/Bio/Tree/Draw
-@dirrm %%SITE_PERL%%/Bio/Tree
-@dirrm %%SITE_PERL%%/Bio/TreeIO
-@dirrm %%SITE_PERL%%/Bio/Variation/IO
-@dirrm %%SITE_PERL%%/Bio/Variation
-@dirrm %%DATADIR%%/models
-@dirrm %%DATADIR%%/scripts/Bio-DB-GFF
-@dirrm %%DATADIR%%/scripts/Bio-DB-SeqFeature-Store
-@dirrm %%DATADIR%%/scripts/DB
-@dirrm %%DATADIR%%/scripts/DB-HIV
-@dirrm %%DATADIR%%/scripts/das
-@dirrm %%DATADIR%%/scripts/index
-@dirrm %%DATADIR%%/scripts/popgen
-@dirrm %%DATADIR%%/scripts/searchio
-@dirrm %%DATADIR%%/scripts/seq
-@dirrm %%DATADIR%%/scripts/seqstats
-@dirrm %%DATADIR%%/scripts/taxa
-@dirrm %%DATADIR%%/scripts/tree
-@dirrm %%DATADIR%%/scripts/utilities
-@dirrm %%DATADIR%%/scripts
-@dirrm %%DATADIR%%
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/Deobfuscator/bin
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/Deobfuscator/cgi-bin
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/Deobfuscator/lib
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/Deobfuscator/t
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/Deobfuscator
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc
-%%PORTDOCS%%@dirrm %%DOCSDIR%%
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/Bio-DB-GFF
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/align
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/cluster
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/contributed
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/db
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/liveseq
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/popgen
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/quality
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/root/lib
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/root
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/searchio
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/sirna
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/structure
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/tk
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/tools
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/tree
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%
diff --git a/biology/paml/pkg-plist b/biology/paml/pkg-plist
index 219d74d..a7eb37b 100644
--- a/biology/paml/pkg-plist
+++ b/biology/paml/pkg-plist
@@ -8,4 +8,3 @@ bin/yn00
 %%PORTDOCS%%%%DOCSDIR%%/pamlDOC.pdf
 %%PORTDOCS%%%%DOCSDIR%%/pamlFAQs.pdf
 %%PORTDOCS%%%%DOCSDIR%%/pamlHistory.txt
-%%PORTDOCS%%@dirrm %%DOCSDIR%%
diff --git a/biology/phylip/pkg-plist b/biology/phylip/pkg-plist
index 6c18e58..b5c9253 100644
--- a/biology/phylip/pkg-plist
+++ b/biology/phylip/pkg-plist
@@ -41,4 +41,3 @@ lib/libdrawtree.so
 %%DATADIR%%/font4
 %%DATADIR%%/font5
 %%DATADIR%%/font6
-@dirrm %%DATADIR%%
diff --git a/biology/platon/pkg-plist b/biology/platon/pkg-plist
index 514d444..fee35f6 100644
--- a/biology/platon/pkg-plist
+++ b/biology/platon/pkg-plist
@@ -72,13 +72,3 @@ bin/pluton
 %%DOCSDIR%%/s913a.res
 %%DOCSDIR%%/sucrose.spf
 %%PORTDOCS%%%%DOCSDIR%%/platon_html.tar.gz
-@dirrm %%DOCSDIR%%/TEST/ABSORB_EXAMPLE
-@dirrm %%DOCSDIR%%/TEST/ABSTOMPA_EXAMPLE
-@dirrm %%DOCSDIR%%/TEST/ABSTOMPA_TEST
-@dirrm %%DOCSDIR%%/TEST/ADDSYM_EXAMPLE
-@dirrm %%DOCSDIR%%/TEST/ASYM_EXAMPLE
-@dirrm %%DOCSDIR%%/TEST/MULABS_EXAMPLE
-@dirrm %%DOCSDIR%%/TEST/PSICOR_EXAMPLE
-@dirrm %%DOCSDIR%%/TEST/SQUEEZE_EXAMPLE
-@dirrm %%DOCSDIR%%/TEST
-@dirrm %%DOCSDIR%%
diff --git a/biology/protomol/pkg-plist b/biology/protomol/pkg-plist
index fffcf8e..0457793 100644
--- a/biology/protomol/pkg-plist
+++ b/biology/protomol/pkg-plist
@@ -112,17 +112,3 @@ bin/xyzviz
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/water_648/water648.spce.par
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/water_648/water648.spce.psf
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/water_648/water648.tip3.par
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/coulomb_309
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/alanine_dipeptide_water_184x
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/argon_400
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/bpti_water_1101
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/bpti_water_14281
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/butane_4
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/alanine_dipeptide_23
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/decalanine_66
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/electrons_22
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/methane_ethane_xxx
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/testset
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/water_216
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/water_648
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%
diff --git a/biology/ruby-bio/pkg-plist b/biology/ruby-bio/pkg-plist
index 76edcc3..73749a2 100644
--- a/biology/ruby-bio/pkg-plist
+++ b/biology/ruby-bio/pkg-plist
@@ -330,65 +330,3 @@ bin/br_bioflat
 bin/br_biogetseq
 bin/br_pmfetch
 etc/bioinformatics/seqdatabase.ini.sample
-@dirrm etc/bioinformatics
-@dirrm %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/single_strand
-@dirrm %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/range/sequence_range
-@dirrm %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/range
-@dirrm %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/double_stranded
-@dirrm %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme
-@dirrm %%RUBY_SITELIBDIR%%/bio/util/color_scheme
-@dirrm %%RUBY_SITELIBDIR%%/bio/util
-@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates
-@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby
-@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/bioruby/generators
-@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/bioruby
-@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins
-@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/vendor
-@dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails
-@dirrm %%RUBY_SITELIBDIR%%/bio/shell/plugin
-@dirrm %%RUBY_SITELIBDIR%%/bio/shell
-@dirrm %%RUBY_SITELIBDIR%%/bio/sequence
-@dirrm %%RUBY_SITELIBDIR%%/bio/io/flatfile
-@dirrm %%RUBY_SITELIBDIR%%/bio/io/biosql/config
-@dirrm %%RUBY_SITELIBDIR%%/bio/io/biosql
-@dirrm %%RUBY_SITELIBDIR%%/bio/io
-@dirrm %%RUBY_SITELIBDIR%%/bio/db/sanger_chromatogram
-@dirrm %%RUBY_SITELIBDIR%%/bio/db/phyloxml
-@dirrm %%RUBY_SITELIBDIR%%/bio/db/pdb
-@dirrm %%RUBY_SITELIBDIR%%/bio/db/kegg
-@dirrm %%RUBY_SITELIBDIR%%/bio/db/genbank
-@dirrm %%RUBY_SITELIBDIR%%/bio/db/fastq
-@dirrm %%RUBY_SITELIBDIR%%/bio/db/fasta
-@dirrm %%RUBY_SITELIBDIR%%/bio/db/embl
-@dirrm %%RUBY_SITELIBDIR%%/bio/db/biosql
-@dirrm %%RUBY_SITELIBDIR%%/bio/db
-@dirrm %%RUBY_SITELIBDIR%%/bio/data
-@dirrm %%RUBY_SITELIBDIR%%/bio/compat
-@dirrm %%RUBY_SITELIBDIR%%/bio/appl/tmhmm
-@dirrm %%RUBY_SITELIBDIR%%/bio/appl/targetp
-@dirrm %%RUBY_SITELIBDIR%%/bio/appl/spidey
-@dirrm %%RUBY_SITELIBDIR%%/bio/appl/sosui
-@dirrm %%RUBY_SITELIBDIR%%/bio/appl/sim4
-@dirrm %%RUBY_SITELIBDIR%%/bio/appl/psort
-@dirrm %%RUBY_SITELIBDIR%%/bio/appl/phylip
-@dirrm %%RUBY_SITELIBDIR%%/bio/appl/paml/yn00
-@dirrm %%RUBY_SITELIBDIR%%/bio/appl/paml/codeml
-@dirrm %%RUBY_SITELIBDIR%%/bio/appl/paml/baseml
-@dirrm %%RUBY_SITELIBDIR%%/bio/appl/paml
-@dirrm %%RUBY_SITELIBDIR%%/bio/appl/meme/mast
-@dirrm %%RUBY_SITELIBDIR%%/bio/appl/meme
-@dirrm %%RUBY_SITELIBDIR%%/bio/appl/mafft
-@dirrm %%RUBY_SITELIBDIR%%/bio/appl/iprscan
-@dirrm %%RUBY_SITELIBDIR%%/bio/appl/hmmer
-@dirrm %%RUBY_SITELIBDIR%%/bio/appl/genscan
-@dirrm %%RUBY_SITELIBDIR%%/bio/appl/gcg
-@dirrm %%RUBY_SITELIBDIR%%/bio/appl/fasta
-@dirrm %%RUBY_SITELIBDIR%%/bio/appl/clustalw
-@dirrm %%RUBY_SITELIBDIR%%/bio/appl/blat
-@dirrm %%RUBY_SITELIBDIR%%/bio/appl/blast
-@dirrm %%RUBY_SITELIBDIR%%/bio/appl/bl2seq
-@dirrm %%RUBY_SITELIBDIR%%/bio/appl
-@dirrm %%RUBY_SITELIBDIR%%/bio
-@dirrm %%RUBY_EXAMPLESDIR%%/bio
-@dirrm %%RUBY_DOCDIR%%/bio/ja
-@dirrm %%RUBY_DOCDIR%%/bio
diff --git a/biology/seqan/pkg-plist b/biology/seqan/pkg-plist
index 94398b2..4e58283 100644
--- a/biology/seqan/pkg-plist
+++ b/biology/seqan/pkg-plist
@@ -2109,37 +2109,3 @@ include/seqan/version.h
 %%DATADIR%%/gapped_params/results_N73_H.dat
 %%DATADIR%%/gapped_params/results_N74_H.dat
 %%DATADIR%%/gapped_params/results_N75_H.dat
-@dirrm %%DATADIR%%/gapped_params
-@dirrm %%DATADIR%%/docs
-@dirrm %%DATADIR%%
-@dirrm include/seqan/system
-@dirrm include/seqan/store
-@dirrm include/seqan/statistics
-@dirrm include/seqan/sequence_journaled
-@dirrm include/seqan/sequence
-@dirrm include/seqan/seeds2
-@dirrm include/seqan/seeds
-@dirrm include/seqan/score
-@dirrm include/seqan/refinement
-@dirrm include/seqan/random
-@dirrm include/seqan/platform
-@dirrm include/seqan/pipe
-@dirrm include/seqan/parallel
-@dirrm include/seqan/modifier
-@dirrm include/seqan/misc
-@dirrm include/seqan/map
-@dirrm include/seqan/index
-@dirrm include/seqan/graph_types
-@dirrm include/seqan/graph_msa
-@dirrm include/seqan/graph_align
-@dirrm include/seqan/graph_algorithms
-@dirrm include/seqan/find_motif
-@dirrm include/seqan/find2
-@dirrm include/seqan/find
-@dirrm include/seqan/file
-@dirrm include/seqan/consensus
-@dirrm include/seqan/chaining
-@dirrm include/seqan/blast
-@dirrm include/seqan/basic
-@dirrm include/seqan/align
-@dirrm include/seqan
diff --git a/biology/tinker/pkg-plist b/biology/tinker/pkg-plist
index b54913e..82e7a0c 100644
--- a/biology/tinker/pkg-plist
+++ b/biology/tinker/pkg-plist
@@ -607,9 +607,3 @@ bin/xyzsybyl
 %%DATADIR%%/test/water.run
 %%DATADIR%%/test/water.xyz
 %%DATADIR%%/tinker.txt
-@dirrm %%DATADIR%%/test
-@dirrm %%DATADIR%%/params
-@dirrm %%DATADIR%%/bench
-@dirrm %%DATADIR%%
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%
-%%PORTDOCS%%@dirrm %%DOCSDIR%%
diff --git a/biology/ugene/pkg-plist b/biology/ugene/pkg-plist
index 32f15e7..8415e70 100644
--- a/biology/ugene/pkg-plist
+++ b/biology/ugene/pkg-plist
@@ -1430,74 +1430,3 @@ share/pixmaps/ugene.xpm
 %%DATADIR%%/workflow_samples/users/Get the second half of sequence.usa
 %%DATADIR%%/workflow_samples/users/LinkData Fetch.usa
 %%DATADIR%%/workflow_samples/users/QualityFilter.usa
-@dirrm %%DATADIR%%/workflow_samples/users
-@dirrm %%DATADIR%%/workflow_samples/Transcriptomics
-@dirrm %%DATADIR%%/workflow_samples/Scenarios
-@dirrm %%DATADIR%%/workflow_samples/NGS/tuxedo
-@dirrm %%DATADIR%%/workflow_samples/NGS/cistrome
-@dirrm %%DATADIR%%/workflow_samples/NGS
-@dirrm %%DATADIR%%/workflow_samples/HMMER
-@dirrm %%DATADIR%%/workflow_samples/Data merging
-@dirrm %%DATADIR%%/workflow_samples/Data marking
-@dirrm %%DATADIR%%/workflow_samples/Custom elements
-@dirrm %%DATADIR%%/workflow_samples/Conversions
-@dirrm %%DATADIR%%/workflow_samples/Alignment
-@dirrm %%DATADIR%%/workflow_samples
-@dirrm %%DATADIR%%/weight_matrix
-@dirrm %%DATADIR%%/snp_scripts
-@dirrm %%DATADIR%%/sitecon_models/prokaryotic
-@dirrm %%DATADIR%%/sitecon_models/eukaryotic
-@dirrm %%DATADIR%%/sitecon_models
-@dirrm %%DATADIR%%/samples/Swiss-Prot
-@dirrm %%DATADIR%%/samples/Stockholm
-@dirrm %%DATADIR%%/samples/SCF
-@dirrm %%DATADIR%%/samples/Raw
-@dirrm %%DATADIR%%/samples/PDB
-@dirrm %%DATADIR%%/samples/Newick
-@dirrm %%DATADIR%%/samples/MSF
-@dirrm %%DATADIR%%/samples/MMDB
-@dirrm %%DATADIR%%/samples/HMM
-@dirrm %%DATADIR%%/samples/Genbank
-@dirrm %%DATADIR%%/samples/GFF
-@dirrm %%DATADIR%%/samples/FASTQ
-@dirrm %%DATADIR%%/samples/FASTA
-@dirrm %%DATADIR%%/samples/EMBL
-@dirrm %%DATADIR%%/samples/CLUSTALW
-@dirrm %%DATADIR%%/samples/Assembly
-@dirrm %%DATADIR%%/samples/ACE
-@dirrm %%DATADIR%%/samples/ABIF
-@dirrm %%DATADIR%%/samples
-@dirrm %%DATADIR%%/query_samples
-@dirrm %%DATADIR%%/primer3
-@dirrm %%DATADIR%%/position_weight_matrix/UniPROBE/PNAS08
-@dirrm %%DATADIR%%/position_weight_matrix/UniPROBE/NBT06
-@dirrm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09
-@dirrm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08
-@dirrm %%DATADIR%%/position_weight_matrix/UniPROBE
-@dirrm %%DATADIR%%/position_weight_matrix/JASPAR/vertebrates
-@dirrm %%DATADIR%%/position_weight_matrix/JASPAR/urochordates
-@dirrm %%DATADIR%%/position_weight_matrix/JASPAR/plants
-@dirrm %%DATADIR%%/position_weight_matrix/JASPAR/nematodes
-@dirrm %%DATADIR%%/position_weight_matrix/JASPAR/insects
-@dirrm %%DATADIR%%/position_weight_matrix/JASPAR/fungi
-@dirrm %%DATADIR%%/position_weight_matrix/JASPAR
-@dirrm %%DATADIR%%/position_weight_matrix
-%%PORTDOCS%%@dirrm %%DOCSDIR%%
-@dirrm %%DATADIR%%/genome_lengths
-@dirrm %%DATADIR%%/enzymes
-@dirrm %%DATADIR%%/custom_annotations
-@dirrm %%DATADIR%%/cmdline
-@dirrm %%DATADIR%%/biostruct3d_plugin
-@dirrm %%DATADIR%%/back_translation/Yeast
-@dirrm %%DATADIR%%/back_translation/Viruses
-@dirrm %%DATADIR%%/back_translation/Vertebrates
-@dirrm %%DATADIR%%/back_translation/Rodents
-@dirrm %%DATADIR%%/back_translation/Primates
-@dirrm %%DATADIR%%/back_translation/Plants
-@dirrm %%DATADIR%%/back_translation/Mammalia
-@dirrm %%DATADIR%%/back_translation/Invertebrates
-@dirrm %%DATADIR%%/back_translation/Bacteria
-@dirrm %%DATADIR%%/back_translation
-@dirrm %%DATADIR%%
-@dirrm lib/ugene/plugins
-@dirrm lib/ugene