Add NOPORTDOCS support to pkg-plist

11 files changed, 1380 insertions, 1381 deletions

diff --git a/biology/biojava/Makefile b/biology/biojava/Makefile
index 76fe2ff54f1e..001fe38a3ce2 100644
--- a/biology/biojava/Makefile
+++ b/biology/biojava/Makefile
@@ -41,7 +41,7 @@ do-install:
 		${CP} -R ${WRKSRC}/demos ${PREFIX}/share/java/${PKGNAME}/;)
 
 .if !defined(NOPORTDOCS)
-	@(${CP} -R ${WRKSRC}/docs ${PREFIX}/share/java/${PKGNAME})
+	@(${CP} -R ${WRKSRC}/docs ${PREFIX}/share/doc/${PKGNAME})
 .endif)
 
 post-install:
diff --git a/biology/biojava/pkg-plist b/biology/biojava/pkg-plist
index c0c4de8b8630..4075c88d44db 100644
--- a/biology/biojava/pkg-plist
+++ b/biology/biojava/pkg-plist
@@ -1,588 +1,587 @@
 share/java/classes/biojava.jar
 share/java/classes/xml.jar
-share/java/biojava-1.01/LICENSE
-share/java/biojava-1.01/README
-share/java/biojava-1.01/demos/acedb/AceTreeView.java
-share/java/biojava-1.01/demos/acedb/ServeAceAsCorba.java
-share/java/biojava-1.01/demos/acedb/AceClient.java
-share/java/biojava-1.01/demos/acedb/SequenceFetch.java
-share/java/biojava-1.01/demos/gff/GFFFilter.java
-share/java/biojava-1.01/demos/gff/EmblToGffFasta.java
-share/java/biojava-1.01/demos/gff/GFFToFeatures.java
-share/java/biojava-1.01/demos/gff/varC4-2.gff
-share/java/biojava-1.01/demos/gff/AL121903.embl
-share/java/biojava-1.01/demos/seq/db/AddFilesToIndex.java
-share/java/biojava-1.01/demos/seq/db/CreateIndex.java
-share/java/biojava-1.01/demos/seq/db/FetchSequence.java
-share/java/biojava-1.01/demos/seq/db/ListSeqsInIndex.java
-share/java/biojava-1.01/demos/seq/TestGenbank.java
-share/java/biojava-1.01/demos/seq/AL121903.genbank
-share/java/biojava-1.01/demos/seq/TestTranslation.java
-share/java/biojava-1.01/demos/seq/TestEmbl.java
-share/java/biojava-1.01/demos/seq/AL121903.embl
-share/java/biojava-1.01/demos/dist/TestDistribution.java
-share/java/biojava-1.01/demos/dp/PairwiseAlignment.java
-share/java/biojava-1.01/demos/dp/fake.fasta
-share/java/biojava-1.01/demos/dp/ViterbiAlign.java
-share/java/biojava-1.01/demos/dp/package.html
-share/java/biojava-1.01/demos/dp/SearchProfile.java
-share/java/biojava-1.01/demos/dp/fakepromoter.xml
-share/java/biojava-1.01/demos/dp/Dice.java
-share/java/biojava-1.01/demos/BioCorba/CorbaDBServer.java
-share/java/biojava-1.01/demos/BioCorba/ChrI.prom.fasta
-share/java/biojava-1.01/demos/BioCorba/CorbaDBClient.java
-share/java/biojava-1.01/demos/files/AL121903.embl
-share/java/biojava-1.01/demos/files/test.hmm
-share/java/biojava-1.01/demos/files/out.gff
-share/java/biojava-1.01/demos/files/AL121903.genbank
-share/java/biojava-1.01/demos/files/ChrI.prom.fasta
-share/java/biojava-1.01/demos/files/fakepromoter.xml
-share/java/biojava-1.01/demos/files/scoptest.fa
-share/java/biojava-1.01/demos/files/varC4-2.gff
-share/java/biojava-1.01/demos/files/varC4-2.dna
-share/java/biojava-1.01/demos/files/fake.fasta
-share/java/biojava-1.01/demos/symbol/TestAmbiguity.java
-share/java/biojava-1.01/demos/symbol/TestSimpleAlignment.java
-share/java/biojava-1.01/demos/symbol/Tools.java
-share/java/biojava-1.01/demos/symbol/TestOrderNSymbolList.java
-share/java/biojava-1.01/demos/symbol/TestGappedSymbolList.java
-share/java/biojava-1.01/demos/symbol/TestWindowedSymbolList.java
-share/java/biojava-1.01/demos/seqviewer/test.fa
-share/java/biojava-1.01/demos/seqviewer/EmblViewer.java
-share/java/biojava-1.01/demos/seqviewer/TestSequencePanel.java
-share/java/biojava-1.01/docs/api/GNOME/UnknownHolder.html
-share/java/biojava-1.01/docs/api/GNOME/package-tree.html
-share/java/biojava-1.01/docs/api/GNOME/package-frame.html
-share/java/biojava-1.01/docs/api/GNOME/_Unknown_Operations.html
-share/java/biojava-1.01/docs/api/GNOME/Unknown.html
-share/java/biojava-1.01/docs/api/GNOME/_Unknown_Tie.html
-share/java/biojava-1.01/docs/api/GNOME/_UnknownImplBase.html
-share/java/biojava-1.01/docs/api/GNOME/_UnknownStub.html
-share/java/biojava-1.01/docs/api/GNOME/UnknownHelper.html
-share/java/biojava-1.01/docs/api/GNOME/package-summary.html
-share/java/biojava-1.01/docs/api/org/acedb/socket/package-summary.html
-share/java/biojava-1.01/docs/api/org/acedb/socket/package-tree.html
-share/java/biojava-1.01/docs/api/org/acedb/socket/package-frame.html
-share/java/biojava-1.01/docs/api/org/acedb/socket/SocketDriver.html
-share/java/biojava-1.01/docs/api/org/acedb/socket/SocketResultSet.html
-share/java/biojava-1.01/docs/api/org/acedb/staticobj/StaticStringValue.html
-share/java/biojava-1.01/docs/api/org/acedb/staticobj/package-tree.html
-share/java/biojava-1.01/docs/api/org/acedb/staticobj/package-frame.html
-share/java/biojava-1.01/docs/api/org/acedb/staticobj/StaticAceNode.html
-share/java/biojava-1.01/docs/api/org/acedb/staticobj/StaticAceObject.html
-share/java/biojava-1.01/docs/api/org/acedb/staticobj/StaticAceSet.html
-share/java/biojava-1.01/docs/api/org/acedb/staticobj/StaticDateValue.html
-share/java/biojava-1.01/docs/api/org/acedb/staticobj/StaticFloatValue.html
-share/java/biojava-1.01/docs/api/org/acedb/staticobj/StaticIntValue.html
-share/java/biojava-1.01/docs/api/org/acedb/staticobj/StaticModelInclude.html
-share/java/biojava-1.01/docs/api/org/acedb/staticobj/StaticModelNode.html
-share/java/biojava-1.01/docs/api/org/acedb/staticobj/StaticModelReference.html
-share/java/biojava-1.01/docs/api/org/acedb/staticobj/StaticModelType.html
-share/java/biojava-1.01/docs/api/org/acedb/staticobj/StaticReference.html
-share/java/biojava-1.01/docs/api/org/acedb/staticobj/package-summary.html
-share/java/biojava-1.01/docs/api/org/acedb/seq/package-summary.html
-share/java/biojava-1.01/docs/api/org/acedb/seq/package-tree.html
-share/java/biojava-1.01/docs/api/org/acedb/seq/package-frame.html
-share/java/biojava-1.01/docs/api/org/acedb/seq/AceAnnotation.html
-share/java/biojava-1.01/docs/api/org/acedb/seq/AceSequence.html
-share/java/biojava-1.01/docs/api/org/acedb/seq/AceSequenceDB.html
-share/java/biojava-1.01/docs/api/org/acedb/AceElement.html
-share/java/biojava-1.01/docs/api/org/acedb/AceNode.html
-share/java/biojava-1.01/docs/api/org/acedb/AceObject.html
-share/java/biojava-1.01/docs/api/org/acedb/AceSet.html
-share/java/biojava-1.01/docs/api/org/acedb/AceValue.html
-share/java/biojava-1.01/docs/api/org/acedb/Connection.html
-share/java/biojava-1.01/docs/api/org/acedb/Database.html
-share/java/biojava-1.01/docs/api/org/acedb/DateValue.html
-share/java/biojava-1.01/docs/api/org/acedb/Driver.html
-share/java/biojava-1.01/docs/api/org/acedb/FloatValue.html
-share/java/biojava-1.01/docs/api/org/acedb/IntValue.html
-share/java/biojava-1.01/docs/api/org/acedb/ModelInclude.html
-share/java/biojava-1.01/docs/api/org/acedb/ModelNode.html
-share/java/biojava-1.01/docs/api/org/acedb/ModelReference.html
-share/java/biojava-1.01/docs/api/org/acedb/ModelType.html
-share/java/biojava-1.01/docs/api/org/acedb/Reference.html
-share/java/biojava-1.01/docs/api/org/acedb/StringValue.html
-share/java/biojava-1.01/docs/api/org/acedb/Ace.html
-share/java/biojava-1.01/docs/api/org/acedb/AcePerlParser.html
-share/java/biojava-1.01/docs/api/org/acedb/AceURL.html
-share/java/biojava-1.01/docs/api/org/acedb/AceUtils.html
-share/java/biojava-1.01/docs/api/org/acedb/Handler.html
-share/java/biojava-1.01/docs/api/org/acedb/AceException.html
-share/java/biojava-1.01/docs/api/org/acedb/AceURLException.html
-share/java/biojava-1.01/docs/api/org/acedb/package-summary.html
-share/java/biojava-1.01/docs/api/org/acedb/AceError.html
-share/java/biojava-1.01/docs/api/org/acedb/package-tree.html
-share/java/biojava-1.01/docs/api/org/acedb/package-frame.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/UnableToProcess.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/package-tree.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/package-frame.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_AnonymousSeq_Operations.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_PrimarySeq_Operations.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_PrimarySeqDB_Operations.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_PrimarySeqIterator_Operations.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_Seq_Operations.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_SeqDB_Operations.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_SeqFeature_Operations.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_SeqFeatureIterator_Operations.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/AnonymousSeq.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/PrimarySeq.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/PrimarySeqDB.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/PrimarySeqIterator.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/Seq.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/SeqDB.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/SeqFeature.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/SeqFeatureIterator.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_AnonymousSeq_Tie.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_AnonymousSeqImplBase.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_AnonymousSeqStub.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_PrimarySeq_Tie.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_PrimarySeqDB_Tie.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_PrimarySeqDBImplBase.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_PrimarySeqDBStub.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_PrimarySeqImplBase.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_PrimarySeqIterator_Tie.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_PrimarySeqIteratorImplBase.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_PrimarySeqStub.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_PrimarySeqIteratorStub.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_Seq_Tie.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_SeqDB_Tie.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_SeqDBImplBase.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_SeqDBStub.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_SeqFeature_Tie.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_SeqFeatureImplBase.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_SeqFeatureIterator_Tie.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_SeqFeatureIteratorImplBase.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_SeqFeatureIteratorStub.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_SeqFeatureStub.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_SeqImplBase.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/_SeqStub.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/AnonymousSeqHelper.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/AnonymousSeqHolder.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/EndOfStreamHelper.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/EndOfStreamHolder.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/NameValueSet.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/NameValueSetHelper.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/NameValueSetHolder.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/NameValueSetListHelper.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/NameValueSetListHolder.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/OutOfRangeHelper.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/OutOfRangeHolder.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/primaryidListHelper.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/primaryidListHolder.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/PrimarySeqDBHelper.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/PrimarySeqDBHolder.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/PrimarySeqHelper.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/PrimarySeqHolder.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/PrimarySeqIteratorHelper.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/PrimarySeqIteratorHolder.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/RequestTooLargeHelper.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/RequestTooLargeHolder.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/SeqDBHelper.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/SeqDBHolder.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/SeqFeatureHelper.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/SeqFeatureHolder.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/SeqFeatureIteratorHelper.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/SeqFeatureIteratorHolder.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/SeqFeatureListHelper.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/SeqFeatureListHolder.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/SeqHelper.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/SeqHolder.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/SeqType.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/SeqTypeHelper.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/SeqTypeHolder.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/stringListHelper.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/stringListHolder.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/UnableToProcessHelper.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/UnableToProcessHolder.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/EndOfStream.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/OutOfRange.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/RequestTooLarge.html
-share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore/package-summary.html
-share/java/biojava-1.01/docs/api/org/biojava/bio/program/gff/IgnoreRecordException.html
-share/java/biojava-1.01/docs/api/org/biojava/bio/program/gff/package-tree.html
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-share/java/biojava-1.01/docs/api/org/biojava/bio/program/gff/GFFDocumentHandler.html
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-share/java/biojava-1.01/docs/api/org/biojava/bio/program/gff/GFFEntrySet.html
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+%%PORTDOCS%%share/doc/biojava-1.01/docs/api/org/biojava/stats/svm/SMOTrainer.html
+%%PORTDOCS%%share/doc/biojava-1.01/docs/api/org/biojava/stats/svm/NestedKernel.html
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+%%PORTDOCS%%share/doc/biojava-1.01/docs/api/org/biojava/stats/svm/PolynomialKernel.html
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+%%PORTDOCS%%share/doc/biojava-1.01/docs/api/org/biojava/stats/svm/SimpleSVMClassifierModel.html
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+%%PORTDOCS%%share/doc/biojava-1.01/docs/api/org/biojava/stats/svm/SMORegressionTrainer.html
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+%%PORTDOCS%%share/doc/biojava-1.01/docs/api/deprecated-list.html
+%%PORTDOCS%%share/doc/biojava-1.01/docs/api/allclasses-frame.html
+%%PORTDOCS%%share/doc/biojava-1.01/docs/api/index.html
+%%PORTDOCS%%share/doc/biojava-1.01/docs/api/packages.html
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+%%PORTDOCS%%share/doc/biojava-1.01/docs/api/stylesheet.css
+%%PORTDOCS%%share/doc/biojava-1.01/docs/api/index-all.html
 @dirrm share/java/classes
-@dirrm share/java/biojava-1.01/demos/acedb
-@dirrm share/java/biojava-1.01/demos/gff
-@dirrm share/java/biojava-1.01/demos/seq/db
-@dirrm share/java/biojava-1.01/demos/seq
-@dirrm share/java/biojava-1.01/demos/dist
-@dirrm share/java/biojava-1.01/demos/dp
-@dirrm share/java/biojava-1.01/demos/BioCorba
-@dirrm share/java/biojava-1.01/demos/files
-@dirrm share/java/biojava-1.01/demos/symbol
-@dirrm share/java/biojava-1.01/demos/seqviewer
-@dirrm share/java/biojava-1.01/demos
-@dirrm share/java/biojava-1.01/docs/api/GNOME
-@dirrm share/java/biojava-1.01/docs/api/org/acedb/socket
-@dirrm share/java/biojava-1.01/docs/api/org/acedb/staticobj
-@dirrm share/java/biojava-1.01/docs/api/org/acedb/seq
-@dirrm share/java/biojava-1.01/docs/api/org/acedb
-@dirrm share/java/biojava-1.01/docs/api/org/Biocorba/Seqcore
-@dirrm share/java/biojava-1.01/docs/api/org/Biocorba
-@dirrm share/java/biojava-1.01/docs/api/org/biojava/bio/program/gff
-@dirrm share/java/biojava-1.01/docs/api/org/biojava/bio/program
-@dirrm share/java/biojava-1.01/docs/api/org/biojava/bio/dp
-@dirrm share/java/biojava-1.01/docs/api/org/biojava/bio/gui/sequence
-@dirrm share/java/biojava-1.01/docs/api/org/biojava/bio/gui
-@dirrm share/java/biojava-1.01/docs/api/org/biojava/bio/dist
-@dirrm share/java/biojava-1.01/docs/api/org/biojava/bio/search
-@dirrm share/java/biojava-1.01/docs/api/org/biojava/bio/seq/db
-@dirrm share/java/biojava-1.01/docs/api/org/biojava/bio/seq/io
-@dirrm share/java/biojava-1.01/docs/api/org/biojava/bio/seq
-@dirrm share/java/biojava-1.01/docs/api/org/biojava/bio/symbol
-@dirrm share/java/biojava-1.01/docs/api/org/biojava/bio
-@dirrm share/java/biojava-1.01/docs/api/org/biojava/bridge/Biocorba/Seqcore
-@dirrm share/java/biojava-1.01/docs/api/org/biojava/bridge/Biocorba
-@dirrm share/java/biojava-1.01/docs/api/org/biojava/bridge/GNOME
-@dirrm share/java/biojava-1.01/docs/api/org/biojava/bridge
-@dirrm share/java/biojava-1.01/docs/api/org/biojava/stats/svm/tools
-@dirrm share/java/biojava-1.01/docs/api/org/biojava/stats/svm
-@dirrm share/java/biojava-1.01/docs/api/org/biojava/stats
-@dirrm share/java/biojava-1.01/docs/api/org/biojava/utils/contract
-@dirrm share/java/biojava-1.01/docs/api/org/biojava/utils/xml
-@dirrm share/java/biojava-1.01/docs/api/org/biojava/utils
-@dirrm share/java/biojava-1.01/docs/api/org/biojava
-@dirrm share/java/biojava-1.01/docs/api/org
-@dirrm share/java/biojava-1.01/docs/api
-@dirrm share/java/biojava-1.01/docs
-@dirrm share/java/biojava-1.01
-@dirrm share/java
+%%PORTDOCS%%@dirrm share/doc/biojava-1.01/demos/acedb
+%%PORTDOCS%%@dirrm share/doc/biojava-1.01/demos/gff
+%%PORTDOCS%%@dirrm share/doc/biojava-1.01/demos/seq/db
+%%PORTDOCS%%@dirrm share/doc/biojava-1.01/demos/seq
+%%PORTDOCS%%@dirrm share/doc/biojava-1.01/demos/dist
+%%PORTDOCS%%@dirrm share/doc/biojava-1.01/demos/dp
+%%PORTDOCS%%@dirrm share/doc/biojava-1.01/demos/BioCorba
+%%PORTDOCS%%@dirrm share/doc/biojava-1.01/demos/files
+%%PORTDOCS%%@dirrm share/doc/biojava-1.01/demos/symbol
+%%PORTDOCS%%@dirrm share/doc/biojava-1.01/demos/seqviewer
+%%PORTDOCS%%@dirrm share/doc/biojava-1.01/demos
+%%PORTDOCS%%@dirrm share/doc/biojava-1.01/docs/api/GNOME
+%%PORTDOCS%%@dirrm share/doc/biojava-1.01/docs/api/org/acedb/socket
+%%PORTDOCS%%@dirrm share/doc/biojava-1.01/docs/api/org/acedb/staticobj
+%%PORTDOCS%%@dirrm share/doc/biojava-1.01/docs/api/org/acedb/seq
+%%PORTDOCS%%@dirrm share/doc/biojava-1.01/docs/api/org/acedb
+%%PORTDOCS%%@dirrm share/doc/biojava-1.01/docs/api/org/Biocorba/Seqcore
+%%PORTDOCS%%@dirrm share/doc/biojava-1.01/docs/api/org/Biocorba
+%%PORTDOCS%%@dirrm share/doc/biojava-1.01/docs/api/org/biojava/bio/program/gff
+%%PORTDOCS%%@dirrm share/doc/biojava-1.01/docs/api/org/biojava/bio/program
+%%PORTDOCS%%@dirrm share/doc/biojava-1.01/docs/api/org/biojava/bio/dp
+%%PORTDOCS%%@dirrm share/doc/biojava-1.01/docs/api/org/biojava/bio/gui/sequence
+%%PORTDOCS%%@dirrm share/doc/biojava-1.01/docs/api/org/biojava/bio/gui
+%%PORTDOCS%%@dirrm share/doc/biojava-1.01/docs/api/org/biojava/bio/dist
+%%PORTDOCS%%@dirrm share/doc/biojava-1.01/docs/api/org/biojava/bio/search
+%%PORTDOCS%%@dirrm share/doc/biojava-1.01/docs/api/org/biojava/bio/seq/db
+%%PORTDOCS%%@dirrm share/doc/biojava-1.01/docs/api/org/biojava/bio/seq/io
+%%PORTDOCS%%@dirrm share/doc/biojava-1.01/docs/api/org/biojava/bio/seq
+%%PORTDOCS%%@dirrm share/doc/biojava-1.01/docs/api/org/biojava/bio/symbol
+%%PORTDOCS%%@dirrm share/doc/biojava-1.01/docs/api/org/biojava/bio
+%%PORTDOCS%%@dirrm share/doc/biojava-1.01/docs/api/org/biojava/bridge/Biocorba/Seqcore
+%%PORTDOCS%%@dirrm share/doc/biojava-1.01/docs/api/org/biojava/bridge/Biocorba
+%%PORTDOCS%%@dirrm share/doc/biojava-1.01/docs/api/org/biojava/bridge/GNOME
+%%PORTDOCS%%@dirrm share/doc/biojava-1.01/docs/api/org/biojava/bridge
+%%PORTDOCS%%@dirrm share/doc/biojava-1.01/docs/api/org/biojava/stats/svm/tools
+%%PORTDOCS%%@dirrm share/doc/biojava-1.01/docs/api/org/biojava/stats/svm
+%%PORTDOCS%%@dirrm share/doc/biojava-1.01/docs/api/org/biojava/stats
+%%PORTDOCS%%@dirrm share/doc/biojava-1.01/docs/api/org/biojava/utils/contract
+%%PORTDOCS%%@dirrm share/doc/biojava-1.01/docs/api/org/biojava/utils/xml
+%%PORTDOCS%%@dirrm share/doc/biojava-1.01/docs/api/org/biojava/utils
+%%PORTDOCS%%@dirrm share/doc/biojava-1.01/docs/api/org/biojava
+%%PORTDOCS%%@dirrm share/doc/biojava-1.01/docs/api/org
+%%PORTDOCS%%@dirrm share/doc/biojava-1.01/docs/api
+%%PORTDOCS%%@dirrm share/doc/biojava-1.01/docs
+%%PORTDOCS%%@dirrm share/doc/biojava-1.01
diff --git a/biology/fastdnaml/Makefile b/biology/fastdnaml/Makefile
index 494e6a26a907..9a42e40174a1 100644
--- a/biology/fastdnaml/Makefile
+++ b/biology/fastdnaml/Makefile
@@ -25,7 +25,7 @@ do-install:
 post-install:
 .if !defined(NOPORTDOCS)
 	${MKDIR} ${PREFIX}/share/doc/${PORTNAME}
-	${INSTALL_MAN} ${WRKSRC}/docs/*.txt ${PREFIX}/share/doc/${PORTNAME}
+	${INSTALL_DATA} ${WRKSRC}/docs/*.txt ${PREFIX}/share/doc/${PORTNAME}
 .endif
 
 .include <bsd.port.mk>
diff --git a/biology/fastdnaml/pkg-plist b/biology/fastdnaml/pkg-plist
index d2d7d1f04e57..cc19e20c3922 100644
--- a/biology/fastdnaml/pkg-plist
+++ b/biology/fastdnaml/pkg-plist
@@ -32,7 +32,7 @@ bin/fastdnaml/usertree
 bin/fastdnaml/usertrees
 bin/fastdnaml/weights
 bin/fastdnaml/weights_categories
-share/doc/fastdnaml/fastDNAml_doc_1.2.txt
-share/doc/fastdnaml/fastDNAml_scripts.txt
+%%PORTDOCS%%share/doc/fastdnaml/fastDNAml_doc_1.2.txt
+%%PORTDOCS%%share/doc/fastdnaml/fastDNAml_scripts.txt
 @dirrm bin/fastdnaml
-@dirrm share/doc/fastdnaml
+%%PORTDOCS%%@dirrm share/doc/fastdnaml
diff --git a/biology/molden/pkg-plist b/biology/molden/pkg-plist
index ed451a6d4716..76ccf186cf28 100644
--- a/biology/molden/pkg-plist
+++ b/biology/molden/pkg-plist
@@ -1,52 +1,52 @@
 bin/molden
-share/doc/molden/figures.ps.Z
-share/doc/molden/manual.ps.Z
-share/doc/molden/manual.txt.Z
-share/molden/test/adf.molf
-share/molden/test/ampac.arc
-share/molden/test/ampac.test
-share/molden/test/bucky.xyz
-share/molden/test/chemx.test
-share/molden/test/complex2.out
-share/molden/test/esp.test
-share/molden/test/esp.txt
-share/molden/test/esp.xyz
-share/molden/test/fragment
-share/molden/test/gamess_uk.freq
-share/molden/test/gamess_uk.input
-share/molden/test/gamess_uk.test1
-share/molden/test/gamess_uk.test2
-share/molden/test/gamess_us.h2o_631g_opt.out
-share/molden/test/gamess_us.irc
-share/molden/test/gamess_us_uhf_opt
-share/molden/test/gaussian.freq
-share/molden/test/gaussian.input
-share/molden/test/gaussian.test
-share/molden/test/jaguar.cube
-share/molden/test/mopac.freq
-share/molden/test/mopac.test
-share/molden/test/pdb.test
-share/molden/test/reacpth.xyz
-share/molden/test/shelx.ins
-share/molden/test/surface.molf
-share/molden/test/test.fdat
-share/molden/test/test.mol2
-share/molden/test/test_homo.cube
-share/molden/test/tinker_charmm.xyz
-share/molden/test/tinker_mm3.xyz
-share/molden/test/uracil.fdat
-share/molden/test/uracil_gauss.out
-share/molden/test/vamp.test
-share/molden/utils/INFO
-share/molden/utils/ch_backspace
-share/molden/utils/ch_mxcon
-share/molden/utils/ch_par
-share/molden/utils/colors
-share/molden/utils/ircextract.awk
-share/molden/utils/molden
-share/molden/utils/multi_vrml.csh
-share/molden/utils/multi_vrml_orbitals.csh
-@dirrm share/molden/test
-@dirrm share/molden/utils
-@dirrm share/molden
-@dirrm share/doc/molden
+%%PORTDOCS%%share/doc/molden/figures.ps.Z
+%%PORTDOCS%%share/doc/molden/manual.ps.Z
+%%PORTDOCS%%share/doc/molden/manual.txt.Z
+%%PORTDOCS%%share/molden/test/adf.molf
+%%PORTDOCS%%share/molden/test/ampac.arc
+%%PORTDOCS%%share/molden/test/ampac.test
+%%PORTDOCS%%share/molden/test/bucky.xyz
+%%PORTDOCS%%share/molden/test/chemx.test
+%%PORTDOCS%%share/molden/test/complex2.out
+%%PORTDOCS%%share/molden/test/esp.test
+%%PORTDOCS%%share/molden/test/esp.txt
+%%PORTDOCS%%share/molden/test/esp.xyz
+%%PORTDOCS%%share/molden/test/fragment
+%%PORTDOCS%%share/molden/test/gamess_uk.freq
+%%PORTDOCS%%share/molden/test/gamess_uk.input
+%%PORTDOCS%%share/molden/test/gamess_uk.test1
+%%PORTDOCS%%share/molden/test/gamess_uk.test2
+%%PORTDOCS%%share/molden/test/gamess_us.h2o_631g_opt.out
+%%PORTDOCS%%share/molden/test/gamess_us.irc
+%%PORTDOCS%%share/molden/test/gamess_us_uhf_opt
+%%PORTDOCS%%share/molden/test/gaussian.freq
+%%PORTDOCS%%share/molden/test/gaussian.input
+%%PORTDOCS%%share/molden/test/gaussian.test
+%%PORTDOCS%%share/molden/test/jaguar.cube
+%%PORTDOCS%%share/molden/test/mopac.freq
+%%PORTDOCS%%share/molden/test/mopac.test
+%%PORTDOCS%%share/molden/test/pdb.test
+%%PORTDOCS%%share/molden/test/reacpth.xyz
+%%PORTDOCS%%share/molden/test/shelx.ins
+%%PORTDOCS%%share/molden/test/surface.molf
+%%PORTDOCS%%share/molden/test/test.fdat
+%%PORTDOCS%%share/molden/test/test.mol2
+%%PORTDOCS%%share/molden/test/test_homo.cube
+%%PORTDOCS%%share/molden/test/tinker_charmm.xyz
+%%PORTDOCS%%share/molden/test/tinker_mm3.xyz
+%%PORTDOCS%%share/molden/test/uracil.fdat
+%%PORTDOCS%%share/molden/test/uracil_gauss.out
+%%PORTDOCS%%share/molden/test/vamp.test
+%%PORTDOCS%%share/molden/utils/INFO
+%%PORTDOCS%%share/molden/utils/ch_backspace
+%%PORTDOCS%%share/molden/utils/ch_mxcon
+%%PORTDOCS%%share/molden/utils/ch_par
+%%PORTDOCS%%share/molden/utils/colors
+%%PORTDOCS%%share/molden/utils/ircextract.awk
+%%PORTDOCS%%share/molden/utils/molden
+%%PORTDOCS%%share/molden/utils/multi_vrml.csh
+%%PORTDOCS%%share/molden/utils/multi_vrml_orbitals.csh
+%%PORTDOCS%%@dirrm share/molden/test
+%%PORTDOCS%%@dirrm share/molden/utils
+%%PORTDOCS%%@dirrm share/molden
+%%PORTDOCS%%@dirrm share/doc/molden
diff --git a/biology/mopac/pkg-plist b/biology/mopac/pkg-plist
index c5b16ce925c0..7a49ffbf6757 100644
--- a/biology/mopac/pkg-plist
+++ b/biology/mopac/pkg-plist
@@ -1,19 +1,19 @@
 bin/MOPAC7
 bin/rmopac
-share/doc/mopac/mopac.tex
-share/doc/mopac/mopac.dvi
-share/examples/mopac/h2o.dat
-share/mopac/test/test_cos.dat
-share/mopac/test/test_cos.out
-share/mopac/test/test_ef_.dat
-share/mopac/test/test_ef_.out
-share/mopac/test/test_gre.dat
-share/mopac/test/test_gre.end
-share/mopac/test/test_gre.out
-share/mopac/test/test_pol.dat
-share/mopac/test/test_pol.out
-share/mopac/test/test.csh
-@dirrm share/examples/mopac
-@dirrm share/doc/mopac
-@dirrm share/mopac/test
-@dirrm share/mopac
+%%PORTDOCS%%share/doc/mopac/mopac.tex
+%%PORTDOCS%%share/doc/mopac/mopac.dvi
+%%PORTDOCS%%share/examples/mopac/h2o.dat
+%%PORTDOCS%%share/mopac/test/test_cos.dat
+%%PORTDOCS%%share/mopac/test/test_cos.out
+%%PORTDOCS%%share/mopac/test/test_ef_.dat
+%%PORTDOCS%%share/mopac/test/test_ef_.out
+%%PORTDOCS%%share/mopac/test/test_gre.dat
+%%PORTDOCS%%share/mopac/test/test_gre.end
+%%PORTDOCS%%share/mopac/test/test_gre.out
+%%PORTDOCS%%share/mopac/test/test_pol.dat
+%%PORTDOCS%%share/mopac/test/test_pol.out
+%%PORTDOCS%%share/mopac/test/test.csh
+%%PORTDOCS%%@dirrm share/examples/mopac
+%%PORTDOCS%%@dirrm share/doc/mopac
+%%PORTDOCS%%@dirrm share/mopac/test
+%%PORTDOCS%%@dirrm share/mopac
diff --git a/biology/psi88/Makefile b/biology/psi88/Makefile
index 36654e4ca86a..e814c3c2b8ba 100644
--- a/biology/psi88/Makefile
+++ b/biology/psi88/Makefile
@@ -29,9 +29,9 @@ post-install:
 .if !defined(NOPORTDOCS)
 	${MKDIR} ${PREFIX}/share/doc/psi88
 	${MKDIR} ${PREFIX}/share/doc/psi88/examples
-	${INSTALL_MAN} ${WRKDIR}/${DISTNAME}/README ${PREFIX}/share/doc/psi88
-	${INSTALL_MAN} ${WRKDIR}/${DISTNAME}/psi88.doc ${PREFIX}/share/doc/psi88
-	${INSTALL_MAN} ${WRKDIR}/${DISTNAME}/examples/* ${PREFIX}/share/doc/psi88/examples
+	@${INSTALL_DATA} ${WRKDIR}/${DISTNAME}/README ${PREFIX}/share/doc/psi88
+	@${INSTALL_DATA} ${WRKDIR}/${DISTNAME}/psi88.doc ${PREFIX}/share/doc/psi88
+	@${INSTALL_DATA} ${WRKDIR}/${DISTNAME}/examples/* ${PREFIX}/share/doc/psi88/examples
 .endif
 
 .include <bsd.port.mk>
diff --git a/biology/psi88/pkg-plist b/biology/psi88/pkg-plist
index ce0007c57359..1c5f1e9f5714 100644
--- a/biology/psi88/pkg-plist
+++ b/biology/psi88/pkg-plist
@@ -9,22 +9,22 @@ bin/preplot
 bin/rpsi1
 bin/rpsi2
 bin/rpsicon
-share/doc/psi88/psi88.doc
-share/doc/psi88/README
-share/doc/psi88/examples/ad634a.psi1
-share/doc/psi88/examples/ad634a.psi2
-share/doc/psi88/examples/ad634a.psicon
-share/doc/psi88/examples/ad635a.psi1
-share/doc/psi88/examples/ad635a.psi2
-share/doc/psi88/examples/ad635a.psicon
-share/doc/psi88/examples/ad636a.psi1
-share/doc/psi88/examples/ad636a.psi2
-share/doc/psi88/examples/ad636a.psicon
-share/doc/psi88/examples/ch3cl.psi1
-share/doc/psi88/examples/ch3cl.psi2
-share/doc/psi88/examples/ch3cl.psicon
-share/doc/psi88/examples/test.psi1
-share/doc/psi88/examples/test.psi2
-share/doc/psi88/examples/test.psicon
-@dirrm share/doc/psi88/examples
-@dirrm share/doc/psi88
+%%PORTDOCS%%share/doc/psi88/psi88.doc
+%%PORTDOCS%%share/doc/psi88/README
+%%PORTDOCS%%share/doc/psi88/examples/ad634a.psi1
+%%PORTDOCS%%share/doc/psi88/examples/ad634a.psi2
+%%PORTDOCS%%share/doc/psi88/examples/ad634a.psicon
+%%PORTDOCS%%share/doc/psi88/examples/ad635a.psi1
+%%PORTDOCS%%share/doc/psi88/examples/ad635a.psi2
+%%PORTDOCS%%share/doc/psi88/examples/ad635a.psicon
+%%PORTDOCS%%share/doc/psi88/examples/ad636a.psi1
+%%PORTDOCS%%share/doc/psi88/examples/ad636a.psi2
+%%PORTDOCS%%share/doc/psi88/examples/ad636a.psicon
+%%PORTDOCS%%share/doc/psi88/examples/ch3cl.psi1
+%%PORTDOCS%%share/doc/psi88/examples/ch3cl.psi2
+%%PORTDOCS%%share/doc/psi88/examples/ch3cl.psicon
+%%PORTDOCS%%share/doc/psi88/examples/test.psi1
+%%PORTDOCS%%share/doc/psi88/examples/test.psi2
+%%PORTDOCS%%share/doc/psi88/examples/test.psicon
+%%PORTDOCS%%@dirrm share/doc/psi88/examples
+%%PORTDOCS%%@dirrm share/doc/psi88
diff --git a/biology/tinker/pkg-plist b/biology/tinker/pkg-plist
index 4253b71400d9..afba39f57dc1 100644
--- a/biology/tinker/pkg-plist
+++ b/biology/tinker/pkg-plist
@@ -48,348 +48,348 @@ bin/xyzedit
 bin/xyzint
 bin/xyzpdb
 bin/xyzsybyl
-share/doc/tinker/README
-share/doc/tinker/announce.txt
-share/doc/tinker/guide.pdf
-share/doc/tinker/guide.ps.gz
-share/doc/tinker/guide.txt
-share/doc/tinker/license.pdf
-share/doc/tinker/license.ps
-share/doc/tinker/license.txt
-share/doc/tinker/logo.pdf
-share/doc/tinker/logo.ps.gz
-share/doc/tinker/summary.pdf
-share/doc/tinker/summary.ps
-share/doc/tinker/summary.txt
-share/examples/tinker/README
-share/examples/tinker/anion.dat
-share/examples/tinker/anion.dyn0
-share/examples/tinker/anion.key
-share/examples/tinker/anion.log
-share/examples/tinker/anion.run
-share/examples/tinker/anion.xyz
-share/examples/tinker/argon.1st
-share/examples/tinker/argon.key
-share/examples/tinker/argon.log
-share/examples/tinker/argon.run
-share/examples/tinker/clean.make
-share/examples/tinker/cluster.dat
-share/examples/tinker/cluster.key
-share/examples/tinker/cluster.log
-share/examples/tinker/cluster.run
-share/examples/tinker/cluster.xyz
-share/examples/tinker/crambin.key
-share/examples/tinker/crambin.log
-share/examples/tinker/crambin.pdb
-share/examples/tinker/crambin.run
-share/examples/tinker/cyclohex.boat
-share/examples/tinker/cyclohex.chair
-share/examples/tinker/cyclohex.key
-share/examples/tinker/cyclohex.log
-share/examples/tinker/cyclohex.run
-share/examples/tinker/enkephalin.dat
-share/examples/tinker/enkephalin.key
-share/examples/tinker/enkephalin.log
-share/examples/tinker/enkephalin.run
-share/examples/tinker/formamide.cell
-share/examples/tinker/formamide.dat
-share/examples/tinker/formamide.key
-share/examples/tinker/formamide.log
-share/examples/tinker/formamide.run
-share/examples/tinker/helix.1st
-share/examples/tinker/helix.key
-share/examples/tinker/helix.log
-share/examples/tinker/helix.run
-share/examples/tinker/salt.cell
-share/examples/tinker/salt.key
-share/examples/tinker/salt.log
-share/examples/tinker/salt.run
-share/tinker/bench/bench-1.key
-share/tinker/bench/bench-1.run
-share/tinker/bench/bench-1.xyz
-share/tinker/bench/bench-2.key
-share/tinker/bench/bench-2.run
-share/tinker/bench/bench-2.xyz
-share/tinker/bench/bench-3.key
-share/tinker/bench/bench-3.run
-share/tinker/bench/bench-3.xyz
-share/tinker/bench/bench-4.dyn0
-share/tinker/bench/bench-4.key
-share/tinker/bench/bench-4.log
-share/tinker/bench/bench-4.run
-share/tinker/bench/bench-4.xyz
-share/tinker/bench/bench-5.dyn0
-share/tinker/bench/bench-5.key
-share/tinker/bench/bench-5.run
-share/tinker/bench/bench-5.xyz
-share/tinker/bench/results-2.3
-share/tinker/bench/results-2.4
-share/tinker/bench/results-2.9
-share/tinker/bench/results-3.1
-share/tinker/bench/results-3.2
-share/tinker/bench/results-3.4
-share/tinker/bench/results-3.5
-share/tinker/bench/results-3.7
-share/tinker/bench/results-3.8
-share/tinker/params/README
-share/tinker/params/amber.prm
-share/tinker/params/amberN.prm
-share/tinker/params/charmm.prm
-share/tinker/params/emr.prm
-share/tinker/params/hoch.prm
-share/tinker/params/mm2.prm
-share/tinker/params/mm3.prm
-share/tinker/params/mm3pro.prm
-share/tinker/params/opls.prm
-share/tinker/params/oplsaa.prm
-share/tinker/params/smooth.prm
-share/tinker/params/smoothaa.prm
-share/tinker/params/tinker.prm
-share/tinker/params/water.prm
-share/tinker/test/README
-share/tinker/test/ala20.key
-share/tinker/test/ala20.xyz
-share/tinker/test/alkane.key
-share/tinker/test/alkane.xyz
-share/tinker/test/arach.int
-share/tinker/test/arach.key
-share/tinker/test/arach.xyz
-share/tinker/test/azulene.int
-share/tinker/test/azulene.key
-share/tinker/test/azulene.xyz
-share/tinker/test/bdna.int
-share/tinker/test/bdna.key
-share/tinker/test/bdna.make
-share/tinker/test/bdna.seq
-share/tinker/test/bdna.xyz
-share/tinker/test/bearing.key
-share/tinker/test/bearing.pdb
-share/tinker/test/bearing.xyz
-share/tinker/test/bearing2.key
-share/tinker/test/bearing2.pdb
-share/tinker/test/bearing2.xyz
-share/tinker/test/benzene.int
-share/tinker/test/benzene.key
-share/tinker/test/benzene.xyz
-share/tinker/test/bowl.int
-share/tinker/test/bowl.key
-share/tinker/test/bowl.xyz
-share/tinker/test/bowl2.key
-share/tinker/test/bowl2.xyz
-share/tinker/test/bowl3.key
-share/tinker/test/bowl3.xyz
-share/tinker/test/butane.int
-share/tinker/test/butane.key
-share/tinker/test/butane.xyz
-share/tinker/test/butane2.int
-share/tinker/test/butane2.key
-share/tinker/test/butane2.xyz
-share/tinker/test/butanes.dyn
-share/tinker/test/butanes.key
-share/tinker/test/butanes.xyz
-share/tinker/test/butanex.key
-share/tinker/test/butanex.xyz
-share/tinker/test/butopls.int
-share/tinker/test/butopls.key
-share/tinker/test/butopls.xyz
-share/tinker/test/butopls2.int
-share/tinker/test/butopls2.key
-share/tinker/test/butopls2.xyz
-share/tinker/test/c5.key
-share/tinker/test/c5.seq
-share/tinker/test/c5.xyz
-share/tinker/test/c7ax.key
-share/tinker/test/c7ax.seq
-share/tinker/test/c7ax.xyz
-share/tinker/test/c7eq.key
-share/tinker/test/c7eq.seq
-share/tinker/test/c7eq.xyz
-share/tinker/test/calmodulin.key
-share/tinker/test/calmodulin.pdb
-share/tinker/test/calmodulin.seq
-share/tinker/test/calmodulin.xyz
-share/tinker/test/cpentene.key
-share/tinker/test/cpentene.xyz
-share/tinker/test/crambin.key
-share/tinker/test/crambin.min
-share/tinker/test/crambin.pdb
-share/tinker/test/crambin.seq
-share/tinker/test/crambin.super
-share/tinker/test/crambin.xyz
-share/tinker/test/crambinx.key
-share/tinker/test/crambinx.ray
-share/tinker/test/crambinx.xyz
-share/tinker/test/crown.int
-share/tinker/test/crown.key
-share/tinker/test/crown.xyz
-share/tinker/test/cychept.int
-share/tinker/test/cychept.key
-share/tinker/test/cychept.xyz
-share/tinker/test/cyclo.int
-share/tinker/test/cyclo.key
-share/tinker/test/cyclo.xyz
-share/tinker/test/cyclo2.int
-share/tinker/test/cyclo2.key
-share/tinker/test/cyclo2.xyz
-share/tinker/test/diene.int
-share/tinker/test/diene.key
-share/tinker/test/diene.xyz
-share/tinker/test/dimethane.key
-share/tinker/test/dimethane.xyz
-share/tinker/test/diwater.key
-share/tinker/test/diwater.lin
-share/tinker/test/diwater.min
-share/tinker/test/diwater.xyz
-share/tinker/test/enkephalin.int
-share/tinker/test/enkephalin.key
-share/tinker/test/enkephalin.make
-share/tinker/test/enkephalin.seq
-share/tinker/test/enkephalin.xyz
-share/tinker/test/ermer.int
-share/tinker/test/ermer.key
-share/tinker/test/ermer.xyz
-share/tinker/test/ester.key
-share/tinker/test/ester.xyz
-share/tinker/test/ethane.int
-share/tinker/test/ethane.key
-share/tinker/test/ethane.xyz
-share/tinker/test/ethanol.int
-share/tinker/test/ethanol.key
-share/tinker/test/ethanol.xyz
-share/tinker/test/ethylene.int
-share/tinker/test/ethylene.key
-share/tinker/test/ethylene.xyz
-share/tinker/test/flane.int
-share/tinker/test/flane.key
-share/tinker/test/flane.xyz
-share/tinker/test/form.key
-share/tinker/test/form.xyz
-share/tinker/test/formbig.key
-share/tinker/test/formbig.xyz
-share/tinker/test/formbox.key
-share/tinker/test/formbox.xyz
-share/tinker/test/furan.int
-share/tinker/test/furan.key
-share/tinker/test/furan.xyz
-share/tinker/test/glucose.key
-share/tinker/test/glucose.xyz
-share/tinker/test/helix.key
-share/tinker/test/helix.xyz
-share/tinker/test/hexane.int
-share/tinker/test/hexane.key
-share/tinker/test/hexane.xyz
-share/tinker/test/hexanes.dyn
-share/tinker/test/hexanes.key
-share/tinker/test/hexanes.run
-share/tinker/test/hexanes.xyz
-share/tinker/test/imidazole.int
-share/tinker/test/imidazole.key
-share/tinker/test/imidazole.xyz
-share/tinker/test/imine.int
-share/tinker/test/imine.key
-share/tinker/test/imine.xyz
-share/tinker/test/lactam.key
-share/tinker/test/lactam.xyz
-share/tinker/test/melittin.key
-share/tinker/test/melittin.pdb
-share/tinker/test/melittin.seq
-share/tinker/test/melittin.xyz
-share/tinker/test/methane.int
-share/tinker/test/methane.key
-share/tinker/test/methane.xyz
-share/tinker/test/methanol.key
-share/tinker/test/methanol.xyz
-share/tinker/test/nacl.key
-share/tinker/test/nacl.xyz
-share/tinker/test/naphthalene.key
-share/tinker/test/naphthalene.xyz
-share/tinker/test/nma.int
-share/tinker/test/nma.key
-share/tinker/test/nma.xyz
-share/tinker/test/nmabox.dyn
-share/tinker/test/nmabox.key
-share/tinker/test/nmabox.xyz
-share/tinker/test/nstilbene.int
-share/tinker/test/nstilbene.key
-share/tinker/test/nstilbene.xyz
-share/tinker/test/octane.int
-share/tinker/test/octane.key
-share/tinker/test/octane.xyz
-share/tinker/test/octane2.int
-share/tinker/test/octane2.key
-share/tinker/test/octane2.xyz
-share/tinker/test/octene.key
-share/tinker/test/octene.xyz
-share/tinker/test/palmitate.key
-share/tinker/test/palmitate.xyz
-share/tinker/test/peptide.int
-share/tinker/test/peptide.key
-share/tinker/test/peptide.make
-share/tinker/test/peptide.min
-share/tinker/test/peptide.pdb
-share/tinker/test/peptide.seq
-share/tinker/test/peptide.xyz
-share/tinker/test/phenanth.key
-share/tinker/test/phenanth.xyz
-share/tinker/test/photo.key
-share/tinker/test/photo.pdb
-share/tinker/test/photo.seq
-share/tinker/test/photo.xyz
-share/tinker/test/propane.key
-share/tinker/test/propane.ray
-share/tinker/test/propane.xyz
-share/tinker/test/propellane.int
-share/tinker/test/propellane.key
-share/tinker/test/propellane.xyz
-share/tinker/test/propyne.key
-share/tinker/test/propyne.xyz
-share/tinker/test/pyridine.int
-share/tinker/test/pyridine.key
-share/tinker/test/pyridine.xyz
-share/tinker/test/pyrrole.int
-share/tinker/test/pyrrole.key
-share/tinker/test/pyrrole.xyz
-share/tinker/test/retinoic.key
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+%%PORTDOCS%%share/tinker/tinker.txt
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+%%PORTDOCS%%@dirrm share/examples/tinker
+%%PORTDOCS%%@dirrm share/tinker/bench
+%%PORTDOCS%%@dirrm share/tinker/params
+%%PORTDOCS%%@dirrm share/tinker/test
+%%PORTDOCS%%@dirrm share/tinker
diff --git a/biology/tinker/pkg-plist.viewer b/biology/tinker/pkg-plist.viewer
index ce873ddf3322..d1d741483e17 100644
--- a/biology/tinker/pkg-plist.viewer
+++ b/biology/tinker/pkg-plist.viewer
@@ -51,350 +51,350 @@ bin/xyzedit
 bin/xyzint
 bin/xyzpdb
 bin/xyzsybyl
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-share/doc/tinker/license.txt
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-share/doc/tinker/logo.ps.gz
-share/doc/tinker/summary.pdf
-share/doc/tinker/summary.ps
-share/doc/tinker/summary.txt
-share/examples/tinker/README
-share/examples/tinker/anion.dat
-share/examples/tinker/anion.dyn0
-share/examples/tinker/anion.key
-share/examples/tinker/anion.log
-share/examples/tinker/anion.run
-share/examples/tinker/anion.xyz
-share/examples/tinker/argon.1st
-share/examples/tinker/argon.key
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-share/examples/tinker/argon.run
-share/examples/tinker/clean.make
-share/examples/tinker/cluster.dat
-share/examples/tinker/cluster.key
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-share/examples/tinker/crambin.key
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-share/examples/tinker/crambin.pdb
-share/examples/tinker/crambin.run
-share/examples/tinker/cyclohex.boat
-share/examples/tinker/cyclohex.chair
-share/examples/tinker/cyclohex.key
-share/examples/tinker/cyclohex.log
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-share/examples/tinker/enkephalin.dat
-share/examples/tinker/enkephalin.key
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-share/examples/tinker/enkephalin.run
-share/examples/tinker/formamide.cell
-share/examples/tinker/formamide.dat
-share/examples/tinker/formamide.key
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-share/examples/tinker/formamide.run
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-share/examples/tinker/salt.cell
-share/examples/tinker/salt.key
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+%%PORTDOCS%%share/tinker/test/ethane.key
+%%PORTDOCS%%share/tinker/test/ethane.xyz
+%%PORTDOCS%%share/tinker/test/ethanol.int
+%%PORTDOCS%%share/tinker/test/ethanol.key
+%%PORTDOCS%%share/tinker/test/ethanol.xyz
+%%PORTDOCS%%share/tinker/test/ethylene.int
+%%PORTDOCS%%share/tinker/test/ethylene.key
+%%PORTDOCS%%share/tinker/test/ethylene.xyz
+%%PORTDOCS%%share/tinker/test/flane.int
+%%PORTDOCS%%share/tinker/test/flane.key
+%%PORTDOCS%%share/tinker/test/flane.xyz
+%%PORTDOCS%%share/tinker/test/form.key
+%%PORTDOCS%%share/tinker/test/form.xyz
+%%PORTDOCS%%share/tinker/test/formbig.key
+%%PORTDOCS%%share/tinker/test/formbig.xyz
+%%PORTDOCS%%share/tinker/test/formbox.key
+%%PORTDOCS%%share/tinker/test/formbox.xyz
+%%PORTDOCS%%share/tinker/test/furan.int
+%%PORTDOCS%%share/tinker/test/furan.key
+%%PORTDOCS%%share/tinker/test/furan.xyz
+%%PORTDOCS%%share/tinker/test/glucose.key
+%%PORTDOCS%%share/tinker/test/glucose.xyz
+%%PORTDOCS%%share/tinker/test/helix.key
+%%PORTDOCS%%share/tinker/test/helix.xyz
+%%PORTDOCS%%share/tinker/test/hexane.int
+%%PORTDOCS%%share/tinker/test/hexane.key
+%%PORTDOCS%%share/tinker/test/hexane.xyz
+%%PORTDOCS%%share/tinker/test/hexanes.dyn
+%%PORTDOCS%%share/tinker/test/hexanes.key
+%%PORTDOCS%%share/tinker/test/hexanes.run
+%%PORTDOCS%%share/tinker/test/hexanes.xyz
+%%PORTDOCS%%share/tinker/test/imidazole.int
+%%PORTDOCS%%share/tinker/test/imidazole.key
+%%PORTDOCS%%share/tinker/test/imidazole.xyz
+%%PORTDOCS%%share/tinker/test/imine.int
+%%PORTDOCS%%share/tinker/test/imine.key
+%%PORTDOCS%%share/tinker/test/imine.xyz
+%%PORTDOCS%%share/tinker/test/lactam.key
+%%PORTDOCS%%share/tinker/test/lactam.xyz
+%%PORTDOCS%%share/tinker/test/melittin.key
+%%PORTDOCS%%share/tinker/test/melittin.pdb
+%%PORTDOCS%%share/tinker/test/melittin.seq
+%%PORTDOCS%%share/tinker/test/melittin.xyz
+%%PORTDOCS%%share/tinker/test/methane.int
+%%PORTDOCS%%share/tinker/test/methane.key
+%%PORTDOCS%%share/tinker/test/methane.xyz
+%%PORTDOCS%%share/tinker/test/methanol.key
+%%PORTDOCS%%share/tinker/test/methanol.xyz
+%%PORTDOCS%%share/tinker/test/nacl.key
+%%PORTDOCS%%share/tinker/test/nacl.xyz
+%%PORTDOCS%%share/tinker/test/naphthalene.key
+%%PORTDOCS%%share/tinker/test/naphthalene.xyz
+%%PORTDOCS%%share/tinker/test/nma.int
+%%PORTDOCS%%share/tinker/test/nma.key
+%%PORTDOCS%%share/tinker/test/nma.xyz
+%%PORTDOCS%%share/tinker/test/nmabox.dyn
+%%PORTDOCS%%share/tinker/test/nmabox.key
+%%PORTDOCS%%share/tinker/test/nmabox.xyz
+%%PORTDOCS%%share/tinker/test/nstilbene.int
+%%PORTDOCS%%share/tinker/test/nstilbene.key
+%%PORTDOCS%%share/tinker/test/nstilbene.xyz
+%%PORTDOCS%%share/tinker/test/octane.int
+%%PORTDOCS%%share/tinker/test/octane.key
+%%PORTDOCS%%share/tinker/test/octane.xyz
+%%PORTDOCS%%share/tinker/test/octane2.int
+%%PORTDOCS%%share/tinker/test/octane2.key
+%%PORTDOCS%%share/tinker/test/octane2.xyz
+%%PORTDOCS%%share/tinker/test/octene.key
+%%PORTDOCS%%share/tinker/test/octene.xyz
+%%PORTDOCS%%share/tinker/test/palmitate.key
+%%PORTDOCS%%share/tinker/test/palmitate.xyz
+%%PORTDOCS%%share/tinker/test/peptide.int
+%%PORTDOCS%%share/tinker/test/peptide.key
+%%PORTDOCS%%share/tinker/test/peptide.make
+%%PORTDOCS%%share/tinker/test/peptide.min
+%%PORTDOCS%%share/tinker/test/peptide.pdb
+%%PORTDOCS%%share/tinker/test/peptide.seq
+%%PORTDOCS%%share/tinker/test/peptide.xyz
+%%PORTDOCS%%share/tinker/test/phenanth.key
+%%PORTDOCS%%share/tinker/test/phenanth.xyz
+%%PORTDOCS%%share/tinker/test/photo.key
+%%PORTDOCS%%share/tinker/test/photo.pdb
+%%PORTDOCS%%share/tinker/test/photo.seq
+%%PORTDOCS%%share/tinker/test/photo.xyz
+%%PORTDOCS%%share/tinker/test/propane.key
+%%PORTDOCS%%share/tinker/test/propane.ray
+%%PORTDOCS%%share/tinker/test/propane.xyz
+%%PORTDOCS%%share/tinker/test/propellane.int
+%%PORTDOCS%%share/tinker/test/propellane.key
+%%PORTDOCS%%share/tinker/test/propellane.xyz
+%%PORTDOCS%%share/tinker/test/propyne.key
+%%PORTDOCS%%share/tinker/test/propyne.xyz
+%%PORTDOCS%%share/tinker/test/pyridine.int
+%%PORTDOCS%%share/tinker/test/pyridine.key
+%%PORTDOCS%%share/tinker/test/pyridine.xyz
+%%PORTDOCS%%share/tinker/test/pyrrole.int
+%%PORTDOCS%%share/tinker/test/pyrrole.key
+%%PORTDOCS%%share/tinker/test/pyrrole.xyz
+%%PORTDOCS%%share/tinker/test/retinoic.key
+%%PORTDOCS%%share/tinker/test/retinoic.xyz
+%%PORTDOCS%%share/tinker/test/sterol.key
+%%PORTDOCS%%share/tinker/test/sterol.xyz
+%%PORTDOCS%%share/tinker/test/styrene.int
+%%PORTDOCS%%share/tinker/test/styrene.key
+%%PORTDOCS%%share/tinker/test/styrene.xyz
+%%PORTDOCS%%share/tinker/test/thiadiene.int
+%%PORTDOCS%%share/tinker/test/thiadiene.key
+%%PORTDOCS%%share/tinker/test/thiadiene.xyz
+%%PORTDOCS%%share/tinker/test/thiophene.int
+%%PORTDOCS%%share/tinker/test/thiophene.key
+%%PORTDOCS%%share/tinker/test/thiophene.xyz
+%%PORTDOCS%%share/tinker/test/thr.int
+%%PORTDOCS%%share/tinker/test/thr.key
+%%PORTDOCS%%share/tinker/test/thr.xyz
+%%PORTDOCS%%share/tinker/test/tip5p.key
+%%PORTDOCS%%share/tinker/test/tip5p.xyz
+%%PORTDOCS%%share/tinker/test/water.int
+%%PORTDOCS%%share/tinker/test/water.key
+%%PORTDOCS%%share/tinker/test/water.xyz
+%%PORTDOCS%%share/tinker/test/waterbig.key
+%%PORTDOCS%%share/tinker/test/waterbig.xyz
+%%PORTDOCS%%share/tinker/test/waterbox.dyn
+%%PORTDOCS%%share/tinker/test/waterbox.key
+%%PORTDOCS%%share/tinker/test/waterbox.xyz
+%%PORTDOCS%%share/tinker/test/waterhuge.key
+%%PORTDOCS%%share/tinker/test/waterhuge.xyz
+%%PORTDOCS%%share/tinker/test/wateroct.dyn
+%%PORTDOCS%%share/tinker/test/wateroct.key
+%%PORTDOCS%%share/tinker/test/wateroct.xyz
+%%PORTDOCS%%share/tinker/test/watersmall.dyn
+%%PORTDOCS%%share/tinker/test/watersmall.key
+%%PORTDOCS%%share/tinker/test/watersmall.xyz
+%%PORTDOCS%%share/tinker/test/white.int
+%%PORTDOCS%%share/tinker/test/white.key
+%%PORTDOCS%%share/tinker/test/white.xyz
+%%PORTDOCS%%share/tinker/tinker.txt
+%%PORTDOCS%%@dirrm share/doc/tinker
+%%PORTDOCS%%@dirrm share/examples/tinker
+%%PORTDOCS%%@dirrm share/tinker/bench
+%%PORTDOCS%%@dirrm share/tinker/params
+%%PORTDOCS%%@dirrm share/tinker/rasmol
+%%PORTDOCS%%@dirrm share/tinker/test
+%%PORTDOCS%%@dirrm share/tinker
diff --git a/biology/xmolwt/pkg-plist b/biology/xmolwt/pkg-plist
index a3966b1cdabe..d9414dad37dd 100644
--- a/biology/xmolwt/pkg-plist
+++ b/biology/xmolwt/pkg-plist
@@ -1,11 +1,11 @@
 bin/gmolwt
 bin/molwt
-share/doc/xmolwt/Howtouse.jp
-share/doc/xmolwt/Readme
-share/doc/xmolwt/Xmolwt
-share/doc/xmolwt/dot.gtkrc
-share/doc/xmolwt/gmolwt.gif
-share/doc/xmolwt/xmolwt-e.html
-share/doc/xmolwt/xmolwt.gif
-share/doc/xmolwt/xmolwt.html
-@dirrm share/doc/xmolwt
+%%PORTDOCS%%share/doc/xmolwt/Howtouse.jp
+%%PORTDOCS%%share/doc/xmolwt/Readme
+%%PORTDOCS%%share/doc/xmolwt/Xmolwt
+%%PORTDOCS%%share/doc/xmolwt/dot.gtkrc
+%%PORTDOCS%%share/doc/xmolwt/gmolwt.gif
+%%PORTDOCS%%share/doc/xmolwt/xmolwt-e.html
+%%PORTDOCS%%share/doc/xmolwt/xmolwt.gif
+%%PORTDOCS%%share/doc/xmolwt/xmolwt.html
+%%PORTDOCS%%@dirrm share/doc/xmolwt