Cleanup

7 files changed, 0 insertions, 1020 deletions

diff --git a/sci-chemistry/jmol/files/12.0.34/jmol-manifest.patch b/sci-chemistry/jmol/files/12.0.34/jmol-manifest.patch
deleted file mode 100644
index 3b43c219d..000000000
--- a/sci-chemistry/jmol/files/12.0.34/jmol-manifest.patch
+++ /dev/null
@@ -1,96 +0,0 @@
-diff -aurN jmol-11.0.3-orig/manifest/applet0.txt jmol-11.0.3/manifest/applet0.txt
---- jmol-11.0.3-orig/manifest/applet0.txt	1969-12-31 18:00:00.000000000 -0600
-+++ jmol-11.0.3/manifest/applet0.txt	2007-05-16 01:54:10.000000000 -0500
-@@ -0,0 +1,6 @@
-+Main-Class: JmolApplet

-+Sealed: true

-+

-+Name: org/jmol/api/

-+Sealed: false

-+

-diff -aurN jmol-11.0.3-orig/manifest/applet1.txt jmol-11.0.3/manifest/applet1.txt
---- jmol-11.0.3-orig/manifest/applet1.txt	1969-12-31 18:00:00.000000000 -0600
-+++ jmol-11.0.3/manifest/applet1.txt	2007-05-16 01:54:10.000000000 -0500
-@@ -0,0 +1,6 @@
-+Name: org/jmol/api/

-+Sealed: false

-+

-+Name: org/jmol/applet/

-+Sealed: true

-+

-diff -aurN jmol-11.0.3-orig/manifest/applet2.txt jmol-11.0.3/manifest/applet2.txt
---- jmol-11.0.3-orig/manifest/applet2.txt	1969-12-31 18:00:00.000000000 -0600
-+++ jmol-11.0.3/manifest/applet2.txt	2007-05-16 01:56:19.000000000 -0500
-@@ -0,0 +1,3 @@
-+Name: javax/vecmath/
-+
-+
-diff -aurN jmol-11.0.3-orig/manifest/applet3.txt jmol-11.0.3/manifest/applet3.txt
---- jmol-11.0.3-orig/manifest/applet3.txt	1969-12-31 18:00:00.000000000 -0600
-+++ jmol-11.0.3/manifest/applet3.txt	2007-05-16 01:56:47.000000000 -0500
-@@ -0,0 +1,4 @@
-+
-+Name: org/jmol/g3d/
-+Sealed: true
-+
-diff -aurN jmol-11.0.3-orig/manifest/applet4.txt jmol-11.0.3/manifest/applet4.txt
---- jmol-11.0.3-orig/manifest/applet4.txt	1969-12-31 18:00:00.000000000 -0600
-+++ jmol-11.0.3/manifest/applet4.txt	2007-05-16 01:57:05.000000000 -0500
-@@ -0,0 +1,4 @@
-+
-+Name: org/jmol/adapter/smarter/
-+Sealed: true
-+
-diff -aurN jmol-11.0.3-orig/manifest/applet5.txt jmol-11.0.3/manifest/applet5.txt
---- jmol-11.0.3-orig/manifest/applet5.txt	1969-12-31 18:00:00.000000000 -0600
-+++ jmol-11.0.3/manifest/applet5.txt	2007-05-16 01:57:23.000000000 -0500
-@@ -0,0 +1,4 @@
-+Name: org/openscience/jmol/ui/
-+Sealed: true
-+
-+
-diff -aurN jmol-11.0.3-orig/manifest/applet6.txt jmol-11.0.3/manifest/applet6.txt
---- jmol-11.0.3-orig/manifest/applet6.txt	1969-12-31 18:00:00.000000000 -0600
-+++ jmol-11.0.3/manifest/applet6.txt	2007-05-16 01:57:46.000000000 -0500
-@@ -0,0 +1,4 @@
-+
-+Name: org/jmol/viewer/
-+Sealed: true
-+
-diff -aurN jmol-11.0.3-orig/manifest/appletMain.txt jmol-11.0.3/manifest/appletMain.txt
---- jmol-11.0.3-orig/manifest/appletMain.txt	1969-12-31 18:00:00.000000000 -0600
-+++ jmol-11.0.3/manifest/appletMain.txt	2007-05-16 01:54:10.000000000 -0500
-@@ -0,0 +1,5 @@
-+Manifest-Version: 1.0

-+Sealed: true

-+

-+Name: org/jmol/api/

-+Sealed: false

-diff -aurN jmol-11.0.3-orig/manifest/appletMonolithic.txt jmol-11.0.3/manifest/appletMonolithic.txt
---- jmol-11.0.3-orig/manifest/appletMonolithic.txt	1969-12-31 18:00:00.000000000 -0600
-+++ jmol-11.0.3/manifest/appletMonolithic.txt	2007-05-16 01:54:10.000000000 -0500
-@@ -0,0 +1,7 @@
-+Main-Class: JmolApplet

-+Sealed: true

-+

-+Name: org/jmol/api/

-+Sealed: false

-+

-+

-diff -aurN jmol-11.0.3-orig/manifest/applet.txt jmol-11.0.3/manifest/applet.txt
---- jmol-11.0.3-orig/manifest/applet.txt	1969-12-31 18:00:00.000000000 -0600
-+++ jmol-11.0.3/manifest/applet.txt	2007-05-16 01:54:10.000000000 -0500
-@@ -0,0 +1,2 @@
-+Manifest-Version: 1.0

-+Sealed: true

-\ No newline at end of file
-diff -aurN jmol-11.0.3-orig/manifest/application.txt jmol-11.0.3/manifest/application.txt
---- jmol-11.0.3-orig/manifest/application.txt	1969-12-31 18:00:00.000000000 -0600
-+++ jmol-11.0.3/manifest/application.txt	2007-05-16 01:54:10.000000000 -0500
-@@ -0,0 +1 @@
-+Main-Class: org.openscience.jmol.app.Jmol

-diff -aurN jmol-11.0.3-orig/manifest/jvxl.txt jmol-11.0.3/manifest/jvxl.txt
---- jmol-11.0.3-orig/manifest/jvxl.txt	1969-12-31 18:00:00.000000000 -0600
-+++ jmol-11.0.3/manifest/jvxl.txt	2007-05-16 01:54:10.000000000 -0500
-@@ -0,0 +1 @@
-+Main-Class: org.openscience.jvxl.Jvxl

diff --git a/sci-chemistry/jmol/files/12.0.34/jmol-nointl.patch b/sci-chemistry/jmol/files/12.0.34/jmol-nointl.patch
deleted file mode 100644
index c1b22e83c..000000000
--- a/sci-chemistry/jmol/files/12.0.34/jmol-nointl.patch
+++ /dev/null
@@ -1,313 +0,0 @@
---- build.xml	2011-02-25 12:59:43.000000000 -0600
-+++ build.xml.new	2011-02-27 12:16:02.398959959 -0600
-@@ -110,10 +110,6 @@
-           <srcfiles dir="doc/source"

-                     includes="JmolGuide.docbook.xml, guide/*.docbook.xml"/>

-         </uptodate>

--        <uptodate targetfile="build/doc/JmolUserGuide_fr/index.html">

--          <srcfiles dir="doc/source"

--                    includes="JmolGuide_fr.docbook.xml, guide/*_fr.docbook.xml"/>

--        </uptodate>

-       </and>

-     </condition>

- 

-@@ -123,14 +119,6 @@
-           <srcfiles dir="doc/source"

-                     includes="JmolHistory.xml,JmolHistoryToHtml.xsl,history/changes.xml" />

-         </uptodate>

--        <uptodate targetfile="build/doc/JmolHistory/ChangeLog_fr.html">

--          <srcfiles dir="doc/source"

--                    includes="JmolHistory_fr.xml,JmolHistoryToHtml.xsl,history/changes_fr.xml" />

--        </uptodate>

--        <uptodate targetfile="build/doc/JmolHistory/ChangeLog_nl.html">

--          <srcfiles dir="doc/source"

--                    includes="JmolHistory_nl.xml,JmolHistoryToHtml.xsl,history/changes_nl.xml" />

--        </uptodate>

-       </and>

-     </condition>

-     

-@@ -140,14 +128,6 @@
-           <srcfiles dir="doc/source"

-                     includes="JmolDevelopersGuide.docbook.xml"/>

-         </uptodate>

--        <uptodate targetfile="build/doc/JmolDevelopersGuide_fr.html">

--          <srcfiles dir="doc/source"

--                    includes="JmolDevelopersGuide_fr.docbook.xml"/>

--        </uptodate>

--        <uptodate targetfile="build/doc/JmolDevelopersGuide_de.html">

--          <srcfiles dir="doc/source"

--                    includes="JmolDevelopersGuide_de.docbook.xml"/>

--        </uptodate>

-       </and>

-     </condition>

- 

-@@ -157,14 +137,6 @@
-           <srcfiles dir="doc/source"

-                     includes="JmolAppletGuide.docbook.xml, applet/*.docbook.xml"/>

-         </uptodate>

--        <uptodate targetfile="build/doc/JmolAppletGuide_fr.html">

--          <srcfiles dir="doc/source"

--                    includes="JmolAppletGuide_fr.docbook.xml, applet/*_fr.docbook.xml"/>

--        </uptodate>

--        <uptodate targetfile="build/doc/JmolAppletGuide_de.html">

--          <srcfiles dir="doc/source"

--                    includes="JmolAppletGuide_de.docbook.xml"/>

--        </uptodate>

-       </and>

-     </condition>

- 

-@@ -385,17 +357,12 @@
-   </target>

- 

-   <target name="jar" id="jar"

--          depends="init,classes,jmolGuide,jmolHistory,jmolDevelopersGuide,libjars,main-i18n">

-+          depends="init,classes,jmolGuide,jmolHistory,jmolDevelopersGuide,libjars">

-     <copy todir="${classes.dir}/org/openscience/jmol/Data/guide" >

-       <fileset dir="build/doc/JmolUserGuide">

-         <include name="**/*.html" />

-       </fileset>

-     </copy>

--    <copy todir="${classes.dir}/org/openscience/jmol/Data/guide_fr" >

--      <fileset dir="build/doc/JmolUserGuide_fr">

--        <include name="**/*.html" />

--      </fileset>

--    </copy>

-     <copy todir="${classes.dir}/org/openscience/jmol/Data" >

-       <fileset dir="build/doc/JmolHistory">

-         <include name="**/*.html" />

-@@ -587,18 +554,6 @@
-       <fileset dir="${appletjars.dir}" includes="**/*"/>

-     </jar>

- 

--    <for list="${all.JmolApplet.languages}" delimiter=","

--         param="current.Jmol.language">

--      <sequential>

--        <jar destfile="${jmol.applet.build.dir}/JmolApplet0_i18n_@{current.Jmol.language}.jar"

--             manifest="manifest/applet_i18n.txt" >

--          <fileset dir="${applet.classes.dir}">

--            <include name="org/jmol/translation/JmolApplet/@{current.Jmol.language}/**" />

--          </fileset>

--        </jar>

--      </sequential>

--    </for>

--

-     <jar destfile="${jmol.applet.build.dir}/JmolApplet0_Minimize.jar" manifest="manifest/applet.txt">

-       <fileset dir="${applet.classes.dir}">

-         <include name="org/jmol/minimize/**" />

-@@ -712,7 +667,6 @@
-         <include name="org/jmol/bspt/**" />

-         <include name="org/jmol/g3d/**" />

-         <include name="org/jmol/geodesic/**" />

--        <include name="org/jmol/i18n/**" />

-         <include name="org/jmol/modelset/**" />

-         <include name="org/jmol/script/**" />

-         <include name="org/jmol/shape/**" />

-@@ -738,7 +692,6 @@
-         <pathelement path="${jmol.applet.build.dir}/JmolApplet0_ShapeSurface.jar" />

-         <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Smiles.jar" />

-         <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Symmetry.jar" />

--        <fileset dir="${jmol.applet.build.dir}" includes="JmolApplet0_i18n_*.jar" />

-       </indexjars>

-     </jar>

-     <!-- changes to this must be replicated below for the signed applet -->

-@@ -851,16 +804,6 @@
-              keystore="selfSignedCertificate/selfSignedCertificate.store"

-              storepass="selfSignedCertificate" alias="selfSignedCertificate" />

- 

--    <for list="${all.JmolApplet.languages}" delimiter=","

--         param="current.Jmol.language">

--      <sequential>

--      	<signjar jar="${jmol.applet.build.dir}/JmolApplet0_i18n_@{current.Jmol.language}.jar"

--                 signedjar="${jmol.applet.build.dir}/JmolAppletSigned0_i18n_@{current.Jmol.language}.jar"

--                 keystore="selfSignedCertificate/selfSignedCertificate.store"

--                 storepass="selfSignedCertificate" alias="selfSignedCertificate" />

--      </sequential>

--    </for>

--

-     <!-- vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv -->

-     <!-- this one must be treated specially because of jar indexing

-          we cannot simply rename the jar file, because the index has

-@@ -906,7 +849,6 @@
-         <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_ShapeSurface.jar" />

-         <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_Smiles.jar" />

-         <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_Symmetry.jar" />

--        <fileset dir="${jmol.applet.build.dir}" includes="JmolAppletSigned0_i18n_*.jar" />

-       </indexjars>

-     </jar>

-     <signjar jar="${jmol.applet.build.dir}/JmolAppletSigned0.jar"

-@@ -944,18 +886,6 @@
- 	      </fileset>

- 	    </jar>

- 

--	    <for list="${all.JmolApplet.languages}" delimiter=","

--	         param="current.Jmol.language">

--	      <sequential>

--	        <jar destfile="${jmol.applet.build.dir}/JmolApplet0_i18n_@{current.Jmol.language}.jar"

--	             manifest="manifest/applet_i18n.txt" >

--	          <fileset dir="${applet.classes.dir}">

--	            <include name="org/jmol/translation/JmolApplet/@{current.Jmol.language}/**" />

--	          </fileset>

--	        </jar>

--	      </sequential>

--	    </for>

--

- 	    <jar destfile="${jmol.applet.build.dir}/JmolApplet0_Minimize.jar" manifest="manifest/applet.txt">

- 	      <fileset dir="${applet.classes.dir}">

- 	        <include name="org/jmol/minimize/**" />

-@@ -1069,7 +999,6 @@
- 	        <include name="org/jmol/bspt/**" />

- 	        <include name="org/jmol/g3d/**" />

- 	        <include name="org/jmol/geodesic/**" />

--	        <include name="org/jmol/i18n/**" />

- 	        <include name="org/jmol/modelset/**" />

- 	        <include name="org/jmol/script/**" />

- 	        <include name="org/jmol/shape/**" />

-@@ -1095,7 +1024,6 @@
- 	        <pathelement path="${jmol.applet.build.dir}/JmolApplet0_ShapeSurface.jar" />

- 	        <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Smiles.jar" />

- 	        <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Symmetry.jar" />

--	        <fileset dir="${jmol.applet.build.dir}" includes="JmolApplet0_i18n_*.jar" />

- 	      </indexjars>

- 	    </jar>

- 	    <!-- changes to this must be replicated below for the signed applet -->

-@@ -1104,7 +1032,7 @@
- 	  </target>

- 

- 	<target name="dist" id="dist"

--          depends="doc,main-i18n,main,signed-applet">

-+          depends="doc,main,signed-applet">

-     <!-- first build binary distribution -->

-     <delete dir="build/dist/jmol-${version}"/>

-     <mkdir dir="build/dist/jmol-${version}"/>

-@@ -1163,7 +1091,6 @@
-       <fileset dir=".">

-         <include name="applet.classes" />

-         <include name="build.xml" />

--        <include name="build-i18n.xml" />

-       </fileset>

-     </copy>

- 

-@@ -1246,7 +1173,6 @@
-       <fileset dir=".">

-         <include name="apisio.classes" />

-         <include name="build.xml" />

--        <include name="build-i18n.xml" />

-       </fileset>

-     </copy>

- 

-@@ -1342,7 +1268,7 @@
-   <target name="xclean" id="xclean">

-   </target>

- 

--  <target name="spotless" id="spotless" depends="clean,spotless-i18n">

-+  <target name="spotless" id="spotless" depends="clean">

-     <delete dir="build"/>

-     <delete dir="${javadoc.dir}"/>

-     <delete dir="packaging/rpm/dist"/>

-@@ -1406,16 +1332,6 @@
-       <arg value="../../../doc/source/JmolGuide.docbook.xml" />

-       <arg value="../../${docbook-xsl}/html/chunk.xsl" />

-     </java>

--    <echo message="Generating user's guide (fr)" />

--    <mkdir dir="build/doc/JmolUserGuide_fr" />

--    <java fork="true" dir="build/doc/JmolUserGuide_fr"

--          classname="com.icl.saxon.StyleSheet"

--          classpath="${lib.dir}/saxon.jar" >

--      <jvmarg value="${proxyHost}" />

--      <jvmarg value="${proxyPort}" />

--      <arg value="../../../doc/source/JmolGuide_fr.docbook.xml" />

--      <arg value="../../${docbook-xsl}/html/chunk.xsl" />

--    </java>

-   </target>

- 

-   <target name="jmolHistory" id="jmolHistory"

-@@ -1430,26 +1346,6 @@
-       <arg value="../../../doc/source/JmolHistory.xml" />

-       <arg value="../../../doc/source/JmolHistoryToHtml.xsl" />

-     </java>

--    <echo message="Generating history of changes (fr)" />

--    <java fork="true" dir="build/doc/JmolHistory"

--          classname="com.icl.saxon.StyleSheet"

--          classpath="${lib.dir}/saxon.jar" >

--      <arg value="-o" />

--      <arg value="ChangeLog_fr.html" />

--      <arg value="../../../doc/source/JmolHistory_fr.xml" />

--      <arg value="../../../doc/source/JmolHistoryToHtml.xsl" />

--      <arg value="lang=fr" />

--    </java>

--    <echo message="Generating history of changes (nl)" />

--    <java fork="true" dir="build/doc/JmolHistory"

--          classname="com.icl.saxon.StyleSheet"

--          classpath="${lib.dir}/saxon.jar" >

--      <arg value="-o" />

--      <arg value="ChangeLog_nl.html" />

--      <arg value="../../../doc/source/JmolHistory_nl.xml" />

--      <arg value="../../../doc/source/JmolHistoryToHtml.xsl" />

--      <arg value="lang=nl" />

--    </java>

-   </target>

- 

-   <target name="jmolDevelopersGuide" id="jmolDevelopersGuide"

-@@ -1463,24 +1359,6 @@
-       <arg value="../../doc/source/JmolDevelopersGuide.docbook.xml" />

-       <arg value="../${docbook-xsl}/html/docbook.xsl" />

-     </java>

--    <echo message="Generating developer's guide (fr)" />

--    <java fork="true" dir="build/doc"

--          classname="com.icl.saxon.StyleSheet"

--          classpath="${lib.dir}/saxon.jar" >

--      <arg value="-o" />

--      <arg value="JmolDevelopersGuide_fr.html" />

--      <arg value="../../doc/source/JmolDevelopersGuide_fr.docbook.xml" />

--      <arg value="../${docbook-xsl}/html/docbook.xsl" />

--    </java>

--    <echo message="Generating developer's guide (de)" />

--    <java fork="true" dir="build/doc"

--          classname="com.icl.saxon.StyleSheet"

--          classpath="${lib.dir}/saxon.jar" >

--      <arg value="-o" />

--      <arg value="JmolDevelopersGuide_de.html" />

--      <arg value="../../doc/source/JmolDevelopersGuide_de.docbook.xml" />

--      <arg value="../${docbook-xsl}/html/docbook.xsl" />

--    </java>

-   </target>

- 

-   <target name="jmolAppletGuide" id="jmolAppletGuide" depends="initdoc"

-@@ -1494,24 +1372,6 @@
-       <arg value="../../doc/source/JmolAppletGuide.docbook.xml" />

-       <arg value="../${docbook-xsl}/html/docbook.xsl" />

-     </java>

--    <echo message="Generating applet guide (fr)" />

--    <java fork="true" dir="build/doc"

--          classname="com.icl.saxon.StyleSheet"

--          classpath="${lib.dir}/saxon.jar" >

--      <arg value="-o" />

--      <arg value="JmolAppletGuide_fr.html" />

--      <arg value="../../doc/source/JmolAppletGuide_fr.docbook.xml" />

--      <arg value="../${docbook-xsl}/html/docbook.xsl" />

--    </java>

--    <echo message="Generating applet guide (de)" />

--    <java fork="true" dir="build/doc"

--          classname="com.icl.saxon.StyleSheet"

--          classpath="${lib.dir}/saxon.jar" >

--      <arg value="-o" />

--      <arg value="JmolAppletGuide_de.html" />

--      <arg value="../../doc/source/JmolAppletGuide_de.docbook.xml" />

--      <arg value="../${docbook-xsl}/html/docbook.xsl" />

--    </java>

-   </target>

- 

-   <target name="test" id="test" depends="main,compile-tests">

-@@ -1543,12 +1403,4 @@
-     <jar destfile="${tests.dir}/Tests.jar" basedir="${test-classes.dir}" />

-   </target>

- 

--  <!-- i18n stuff -->

--  <target name="main-i18n" depends="classes">

--    <ant antfile="tools/build-i18n.xml" target="main-i18n"/>

--  </target>

--  <target name="spotless-i18n">

--    <ant antfile="tools/build-i18n.xml" target="spotless-i18n"/>

--  </target>

--

- </project>

diff --git a/sci-chemistry/jmol/files/jmol-11.6-manifest.patch b/sci-chemistry/jmol/files/jmol-11.6-manifest.patch
deleted file mode 100644
index 3b43c219d..000000000
--- a/sci-chemistry/jmol/files/jmol-11.6-manifest.patch
+++ /dev/null
@@ -1,96 +0,0 @@
-diff -aurN jmol-11.0.3-orig/manifest/applet0.txt jmol-11.0.3/manifest/applet0.txt
---- jmol-11.0.3-orig/manifest/applet0.txt	1969-12-31 18:00:00.000000000 -0600
-+++ jmol-11.0.3/manifest/applet0.txt	2007-05-16 01:54:10.000000000 -0500
-@@ -0,0 +1,6 @@
-+Main-Class: JmolApplet

-+Sealed: true

-+

-+Name: org/jmol/api/

-+Sealed: false

-+

-diff -aurN jmol-11.0.3-orig/manifest/applet1.txt jmol-11.0.3/manifest/applet1.txt
---- jmol-11.0.3-orig/manifest/applet1.txt	1969-12-31 18:00:00.000000000 -0600
-+++ jmol-11.0.3/manifest/applet1.txt	2007-05-16 01:54:10.000000000 -0500
-@@ -0,0 +1,6 @@
-+Name: org/jmol/api/

-+Sealed: false

-+

-+Name: org/jmol/applet/

-+Sealed: true

-+

-diff -aurN jmol-11.0.3-orig/manifest/applet2.txt jmol-11.0.3/manifest/applet2.txt
---- jmol-11.0.3-orig/manifest/applet2.txt	1969-12-31 18:00:00.000000000 -0600
-+++ jmol-11.0.3/manifest/applet2.txt	2007-05-16 01:56:19.000000000 -0500
-@@ -0,0 +1,3 @@
-+Name: javax/vecmath/
-+
-+
-diff -aurN jmol-11.0.3-orig/manifest/applet3.txt jmol-11.0.3/manifest/applet3.txt
---- jmol-11.0.3-orig/manifest/applet3.txt	1969-12-31 18:00:00.000000000 -0600
-+++ jmol-11.0.3/manifest/applet3.txt	2007-05-16 01:56:47.000000000 -0500
-@@ -0,0 +1,4 @@
-+
-+Name: org/jmol/g3d/
-+Sealed: true
-+
-diff -aurN jmol-11.0.3-orig/manifest/applet4.txt jmol-11.0.3/manifest/applet4.txt
---- jmol-11.0.3-orig/manifest/applet4.txt	1969-12-31 18:00:00.000000000 -0600
-+++ jmol-11.0.3/manifest/applet4.txt	2007-05-16 01:57:05.000000000 -0500
-@@ -0,0 +1,4 @@
-+
-+Name: org/jmol/adapter/smarter/
-+Sealed: true
-+
-diff -aurN jmol-11.0.3-orig/manifest/applet5.txt jmol-11.0.3/manifest/applet5.txt
---- jmol-11.0.3-orig/manifest/applet5.txt	1969-12-31 18:00:00.000000000 -0600
-+++ jmol-11.0.3/manifest/applet5.txt	2007-05-16 01:57:23.000000000 -0500
-@@ -0,0 +1,4 @@
-+Name: org/openscience/jmol/ui/
-+Sealed: true
-+
-+
-diff -aurN jmol-11.0.3-orig/manifest/applet6.txt jmol-11.0.3/manifest/applet6.txt
---- jmol-11.0.3-orig/manifest/applet6.txt	1969-12-31 18:00:00.000000000 -0600
-+++ jmol-11.0.3/manifest/applet6.txt	2007-05-16 01:57:46.000000000 -0500
-@@ -0,0 +1,4 @@
-+
-+Name: org/jmol/viewer/
-+Sealed: true
-+
-diff -aurN jmol-11.0.3-orig/manifest/appletMain.txt jmol-11.0.3/manifest/appletMain.txt
---- jmol-11.0.3-orig/manifest/appletMain.txt	1969-12-31 18:00:00.000000000 -0600
-+++ jmol-11.0.3/manifest/appletMain.txt	2007-05-16 01:54:10.000000000 -0500
-@@ -0,0 +1,5 @@
-+Manifest-Version: 1.0

-+Sealed: true

-+

-+Name: org/jmol/api/

-+Sealed: false

-diff -aurN jmol-11.0.3-orig/manifest/appletMonolithic.txt jmol-11.0.3/manifest/appletMonolithic.txt
---- jmol-11.0.3-orig/manifest/appletMonolithic.txt	1969-12-31 18:00:00.000000000 -0600
-+++ jmol-11.0.3/manifest/appletMonolithic.txt	2007-05-16 01:54:10.000000000 -0500
-@@ -0,0 +1,7 @@
-+Main-Class: JmolApplet

-+Sealed: true

-+

-+Name: org/jmol/api/

-+Sealed: false

-+

-+

-diff -aurN jmol-11.0.3-orig/manifest/applet.txt jmol-11.0.3/manifest/applet.txt
---- jmol-11.0.3-orig/manifest/applet.txt	1969-12-31 18:00:00.000000000 -0600
-+++ jmol-11.0.3/manifest/applet.txt	2007-05-16 01:54:10.000000000 -0500
-@@ -0,0 +1,2 @@
-+Manifest-Version: 1.0

-+Sealed: true

-\ No newline at end of file
-diff -aurN jmol-11.0.3-orig/manifest/application.txt jmol-11.0.3/manifest/application.txt
---- jmol-11.0.3-orig/manifest/application.txt	1969-12-31 18:00:00.000000000 -0600
-+++ jmol-11.0.3/manifest/application.txt	2007-05-16 01:54:10.000000000 -0500
-@@ -0,0 +1 @@
-+Main-Class: org.openscience.jmol.app.Jmol

-diff -aurN jmol-11.0.3-orig/manifest/jvxl.txt jmol-11.0.3/manifest/jvxl.txt
---- jmol-11.0.3-orig/manifest/jvxl.txt	1969-12-31 18:00:00.000000000 -0600
-+++ jmol-11.0.3/manifest/jvxl.txt	2007-05-16 01:54:10.000000000 -0500
-@@ -0,0 +1 @@
-+Main-Class: org.openscience.jvxl.Jvxl

diff --git a/sci-chemistry/jmol/files/jmol-11.6-nointl.patch b/sci-chemistry/jmol/files/jmol-11.6-nointl.patch
deleted file mode 100644
index 351093faf..000000000
--- a/sci-chemistry/jmol/files/jmol-11.6-nointl.patch
+++ /dev/null
@@ -1,274 +0,0 @@
---- jmol-11.6/build.xml	2008-10-08 19:03:17.000000000 +0200
-+++ jmol-11.6/build.xml.new	2009-04-23 11:05:58.000000000 +0200
-@@ -100,10 +100,6 @@
-           <srcfiles dir="doc/source"

-                     includes="JmolGuide.docbook.xml, guide/*.docbook.xml"/>

-         </uptodate>

--        <uptodate targetfile="build/doc/JmolUserGuide_fr/index.html">

--          <srcfiles dir="doc/source"

--                    includes="JmolGuide_fr.docbook.xml, guide/*_fr.docbook.xml"/>

--        </uptodate>

-       </and>

-     </condition>

- 

-@@ -113,14 +109,6 @@
-           <srcfiles dir="doc/source"

-                     includes="JmolHistory.xml,JmolHistoryToHtml.xsl,history/changes.xml" />

-         </uptodate>

--        <uptodate targetfile="build/doc/JmolHistory/ChangeLog_fr.html">

--          <srcfiles dir="doc/source"

--                    includes="JmolHistory_fr.xml,JmolHistoryToHtml.xsl,history/changes_fr.xml" />

--        </uptodate>

--        <uptodate targetfile="build/doc/JmolHistory/ChangeLog_nl.html">

--          <srcfiles dir="doc/source"

--                    includes="JmolHistory_nl.xml,JmolHistoryToHtml.xsl,history/changes_nl.xml" />

--        </uptodate>

-       </and>

-     </condition>

-     

-@@ -130,14 +118,6 @@
-           <srcfiles dir="doc/source"

-                     includes="JmolDevelopersGuide.docbook.xml"/>

-         </uptodate>

--        <uptodate targetfile="build/doc/JmolDevelopersGuide_fr.html">

--          <srcfiles dir="doc/source"

--                    includes="JmolDevelopersGuide_fr.docbook.xml"/>

--        </uptodate>

--        <uptodate targetfile="build/doc/JmolDevelopersGuide_de.html">

--          <srcfiles dir="doc/source"

--                    includes="JmolDevelopersGuide_de.docbook.xml"/>

--        </uptodate>

-       </and>

-     </condition>

- 

-@@ -147,14 +127,6 @@
-           <srcfiles dir="doc/source"

-                     includes="JmolAppletGuide.docbook.xml, applet/*.docbook.xml"/>

-         </uptodate>

--        <uptodate targetfile="build/doc/JmolAppletGuide_fr.html">

--          <srcfiles dir="doc/source"

--                    includes="JmolAppletGuide_fr.docbook.xml, applet/*_fr.docbook.xml"/>

--        </uptodate>

--        <uptodate targetfile="build/doc/JmolAppletGuide_de.html">

--          <srcfiles dir="doc/source"

--                    includes="JmolAppletGuide_de.docbook.xml"/>

--        </uptodate>

-       </and>

-     </condition>

- 

-@@ -348,17 +320,12 @@
-   </target>

- 

-   <target name="jar" id="jar"

--          depends="init,classes,jmolGuide,jmolHistory,jmolDevelopersGuide,libjars,main-i18n">

-+          depends="init,classes,jmolGuide,jmolHistory,jmolDevelopersGuide,libjars">

-     <copy todir="${classes.dir}/org/openscience/jmol/Data/guide" >

-       <fileset dir="build/doc/JmolUserGuide">

-         <include name="**/*.html" />

-       </fileset>

-     </copy>

--    <copy todir="${classes.dir}/org/openscience/jmol/Data/guide_fr" >

--      <fileset dir="build/doc/JmolUserGuide_fr">

--        <include name="**/*.html" />

--      </fileset>

--    </copy>

-     <copy todir="${classes.dir}/org/openscience/jmol/Data" >

-       <fileset dir="build/doc/JmolHistory">

-         <include name="**/*.html" />

-@@ -505,11 +472,6 @@
- 	      </fileset>

- 	      <fileset dir="${appletjars.dir}" includes="**/*"/>

- 	    </jar>	

--  	    <jar destfile="${jmol.applet.build.dir}/JmolApplet0_i18n.jar" manifest="manifest/applet_i18n.txt" >

--	      <fileset dir="${applet.classes.dir}">

--	        <include name="org/jmol/translation/**" />

--	      </fileset>

--	    </jar>

- 	  	<jar destfile="${jmol.applet.build.dir}/JmolApplet0_Minimize.jar" manifest="manifest/applet.txt">

- 	      <fileset dir="${applet.classes.dir}">

- 	        <include name="org/jmol/minimize/**" />

-@@ -606,7 +568,6 @@
-   		<include name="org/jmol/bspt/**" />

- 		<include name="org/jmol/g3d/**" />

- 		<include name="org/jmol/geodesic/**" />

--   		<include name="org/jmol/i18n/**" />

-   		<include name="org/jmol/modelset/**" />

-   		<include name="org/jmol/shape/**" />

- 		<include name="org/jmol/util/**" />

-@@ -628,7 +589,6 @@
-         <pathelement path="${jmol.applet.build.dir}/JmolApplet0_ShapeSurface.jar" />

-         <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Smiles.jar" />

-         <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Symmetry.jar" />

--        <pathelement path="${jmol.applet.build.dir}/JmolApplet0_i18n.jar" />

-       </indexjars>

-     </jar>

-     <!-- changes to this must be replicated below for the signed applet -->

-@@ -713,11 +673,6 @@
-              keystore="selfSignedCertificate/selfSignedCertificate.store"

-              storepass="selfSignedCertificate" alias="selfSignedCertificate" />

-     	  	

--  	<signjar jar="${jmol.applet.build.dir}/JmolApplet0_i18n.jar"

--             signedjar="${jmol.applet.build.dir}/JmolAppletSigned0_i18n.jar"

--             keystore="selfSignedCertificate/selfSignedCertificate.store"

--             storepass="selfSignedCertificate" alias="selfSignedCertificate" />

--

-     <!-- vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv -->

-     <!-- this one must be treated specially because of jar indexing

-          we cannot simply rename the jar file, because the index has

-@@ -743,7 +698,6 @@
- 		<include name="org/jmol/shape/**" />

- 		<include name="org/jmol/viewer/**" />

- 		<include name="org/jmol/util/**" />

--		<include name="org/jmol/i18n/**" />

-       </fileset>    	

-       <indexjars>

-         <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_Popup.jar" />

-@@ -757,7 +711,6 @@
-         <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_ShapeSurface.jar" />

-         <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_Smiles.jar" />

-         <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_Symmetry.jar" />

--        <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_i18n.jar" />

-       </indexjars>

-     </jar>

-     <signjar jar="${jmol.applet.build.dir}/JmolAppletSigned0.jar"

-@@ -767,7 +720,7 @@
-   </target>

- 

-   <target name="dist" id="dist"

--          depends="doc,main-i18n,main,signed-applet">

-+          depends="doc,main,signed-applet">

-     <!-- first build binary distribution -->

-     <delete dir="build/dist/jmol-${version}"/>

-     <mkdir dir="build/dist/jmol-${version}"/>

-@@ -824,7 +777,6 @@
-       <fileset dir=".">

-         <include name="applet.classes" />

-         <include name="build.xml" />

--        <include name="build-i18n.xml" />

-       </fileset>

-     </copy>

- 

-@@ -903,7 +855,6 @@
-       <fileset dir=".">

-         <include name="apisio.classes" />

-         <include name="build.xml" />

--        <include name="build-i18n.xml" />

-       </fileset>

-     </copy>

- 

-@@ -995,7 +946,7 @@
-   <target name="xclean" id="xclean">

-   </target>

- 

--  <target name="spotless" id="spotless" depends="clean,spotless-i18n">

-+  <target name="spotless" id="spotless" depends="clean">

-     <delete dir="build"/>

-     <delete dir="${javadoc.dir}"/>

-     <delete dir="packaging/rpm/dist"/>

-@@ -1058,16 +1009,6 @@
-       <arg value="../../../doc/source/JmolGuide.docbook.xml" />

-       <arg value="../../${docbook-xsl}/html/chunk.xsl" />

-     </java>

--    <echo message="Generating user's guide (fr)" />

--    <mkdir dir="build/doc/JmolUserGuide_fr" />

--    <java fork="true" dir="build/doc/JmolUserGuide_fr"

--          classname="com.icl.saxon.StyleSheet"

--          classpath="${lib.dir}/saxon.jar" >

--      <jvmarg value="${proxyHost}" />

--      <jvmarg value="${proxyPort}" />

--      <arg value="../../../doc/source/JmolGuide_fr.docbook.xml" />

--      <arg value="../../${docbook-xsl}/html/chunk.xsl" />

--    </java>

-   </target>

- 

-   <target name="jmolHistory" id="jmolHistory"

-@@ -1082,26 +1023,6 @@
-       <arg value="../../../doc/source/JmolHistory.xml" />

-       <arg value="../../../doc/source/JmolHistoryToHtml.xsl" />

-     </java>

--    <echo message="Generating history of changes (fr)" />

--    <java fork="true" dir="build/doc/JmolHistory"

--          classname="com.icl.saxon.StyleSheet"

--          classpath="${lib.dir}/saxon.jar" >

--      <arg value="-o" />

--      <arg value="ChangeLog_fr.html" />

--      <arg value="../../../doc/source/JmolHistory_fr.xml" />

--      <arg value="../../../doc/source/JmolHistoryToHtml.xsl" />

--      <arg value="lang=fr" />

--    </java>

--    <echo message="Generating history of changes (nl)" />

--    <java fork="true" dir="build/doc/JmolHistory"

--          classname="com.icl.saxon.StyleSheet"

--          classpath="${lib.dir}/saxon.jar" >

--      <arg value="-o" />

--      <arg value="ChangeLog_nl.html" />

--      <arg value="../../../doc/source/JmolHistory_nl.xml" />

--      <arg value="../../../doc/source/JmolHistoryToHtml.xsl" />

--      <arg value="lang=nl" />

--    </java>

-   </target>

- 

-   <target name="jmolDevelopersGuide" id="jmolDevelopersGuide"

-@@ -1115,24 +1036,6 @@
-       <arg value="../../doc/source/JmolDevelopersGuide.docbook.xml" />

-       <arg value="../${docbook-xsl}/html/docbook.xsl" />

-     </java>

--    <echo message="Generating developer's guide (fr)" />

--    <java fork="true" dir="build/doc"

--          classname="com.icl.saxon.StyleSheet"

--          classpath="${lib.dir}/saxon.jar" >

--      <arg value="-o" />

--      <arg value="JmolDevelopersGuide_fr.html" />

--      <arg value="../../doc/source/JmolDevelopersGuide_fr.docbook.xml" />

--      <arg value="../${docbook-xsl}/html/docbook.xsl" />

--    </java>

--    <echo message="Generating developer's guide (de)" />

--    <java fork="true" dir="build/doc"

--          classname="com.icl.saxon.StyleSheet"

--          classpath="${lib.dir}/saxon.jar" >

--      <arg value="-o" />

--      <arg value="JmolDevelopersGuide_de.html" />

--      <arg value="../../doc/source/JmolDevelopersGuide_de.docbook.xml" />

--      <arg value="../${docbook-xsl}/html/docbook.xsl" />

--    </java>

-   </target>

- 

-   <target name="jmolAppletGuide" id="jmolAppletGuide" depends="initdoc"

-@@ -1146,24 +1049,6 @@
-       <arg value="../../doc/source/JmolAppletGuide.docbook.xml" />

-       <arg value="../${docbook-xsl}/html/docbook.xsl" />

-     </java>

--    <echo message="Generating applet guide (fr)" />

--    <java fork="true" dir="build/doc"

--          classname="com.icl.saxon.StyleSheet"

--          classpath="${lib.dir}/saxon.jar" >

--      <arg value="-o" />

--      <arg value="JmolAppletGuide_fr.html" />

--      <arg value="../../doc/source/JmolAppletGuide_fr.docbook.xml" />

--      <arg value="../${docbook-xsl}/html/docbook.xsl" />

--    </java>

--    <echo message="Generating applet guide (de)" />

--    <java fork="true" dir="build/doc"

--          classname="com.icl.saxon.StyleSheet"

--          classpath="${lib.dir}/saxon.jar" >

--      <arg value="-o" />

--      <arg value="JmolAppletGuide_de.html" />

--      <arg value="../../doc/source/JmolAppletGuide_de.docbook.xml" />

--      <arg value="../${docbook-xsl}/html/docbook.xsl" />

--    </java>

-   </target>

- 

-   <target name="test" id="test" depends="main,compile-tests">

-@@ -1195,12 +1080,4 @@
-     <jar destfile="${tests.dir}/Tests.jar" basedir="${test-classes.dir}" />

-   </target>

- 

--  <!-- i18n stuff -->

--  <target name="main-i18n" depends="classes">

--    <ant antfile="build-i18n.xml" target="main-i18n"/>

--  </target>

--  <target name="spotless-i18n">

--    <ant antfile="build-i18n.xml" target="spotless-i18n"/>

--  </target>

--

- </project>

diff --git a/sci-chemistry/jmol/jmol-11.6.ebuild b/sci-chemistry/jmol/jmol-11.6.ebuild
deleted file mode 100644
index 486705db1..000000000
--- a/sci-chemistry/jmol/jmol-11.6.ebuild
+++ /dev/null
@@ -1,119 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=1
-WEBAPP_OPTIONAL="yes"
-
-inherit eutils java-pkg-2 java-ant-2 webapp
-
-DESCRIPTION="Jmol is a java molecular viever for 3-D chemical structures."
-SRC_URI="mirror://sourceforge/${PN}/${P}-full.tar.gz"
-HOMEPAGE="http://jmol.sourceforge.net/"
-KEYWORDS="~x86 ~amd64"
-LICENSE="LGPL-2.1"
-
-IUSE="client-only vhosts"
-
-WEBAPP_MANUAL_SLOT="yes"
-SLOT="0"
-
-COMMON_DEP="dev-java/commons-cli:1
-	dev-java/itext:0
-	sci-libs/jmol-acme:0
-	sci-libs/vecmath-objectclub:0"
-
-RDEPEND=">=virtual/jre-1.4
-	${COMMON_DEP}"
-DEPEND=">=virtual/jdk-1.4
-	!client-only? ( ${WEBAPP_DEPEND} )
-	${COMMON_DEP}"
-
-pkg_setup() {
-
-	if ! use client-only ; then
-		webapp_pkg_setup || die "Failed to setup webapp"
-	fi
-
-	java-pkg-2_pkg_setup
-
-}
-
-src_unpack() {
-
-	unpack ${A}
-	epatch "${FILESDIR}"/${P}-nointl.patch
-	epatch "${FILESDIR}"/${P}-manifest.patch
-
-	mkdir "${S}"/selfSignedCertificate || die "Failed to create Cert directory."
-	cp "${FILESDIR}"/selfSignedCertificate.store "${S}"/selfSignedCertificate/ \
-		|| die "Failed to install Cert file."
-
-	rm -v "${S}"/*.jar "${S}"/plugin-jars/*.jar || die
-	cd "${S}/jars"
-
-# We still have to use netscape.jar on amd64 until a nice way to include plugin.jar comes along.
-	if use amd64; then
-		mv -v netscape.jar netscape.tempjar || die "Failed to move netscape.jar."
-		rm -v *.jar *.tar.gz || die "Failed to remove jars."
-		mv -v netscape.tempjar netscape.jar || die "Failed to move netscape.tempjar."
-	fi
-
-	java-pkg_jar-from vecmath-objectclub vecmath-objectclub.jar vecmath1.2-1.14.jar
-	java-pkg_jar-from itext iText.jar itext-1.4.5.jar
-	java-pkg_jar-from jmol-acme jmol-acme.jar Acme.jar
-	java-pkg_jar-from commons-cli-1 commons-cli.jar commons-cli-1.0.jar
-
-	mkdir -p "${S}/build/appjars" || die
-}
-
-src_compile() {
-	# prevent absorbing dep's classes
-	eant -Dlibjars.uptodate=true main
-}
-
-src_install() {
-
-	java-pkg_dojar build/Jmol.jar
-	dohtml -r  build/doc/* || die "Failed to install html docs."
-	dodoc *.txt doc/*license* || die "Failed to install licenses."
-
-	java-pkg_dolauncher ${PN} --main org.openscience.jmol.app.Jmol \
-		--java_args "-Xmx512m"
-
-	if ! use client-only ; then
-		webapp_src_preinst || die "Failed webapp_src_preinst."
-		cmd="cp Jmol.js build/Jmol.jar "${D}${MY_HTDOCSDIR}"" ; ${cmd} \
-		|| die "${cmd} failed."
-		cmd="cp build/JmolApplet*.jar "${D}${MY_HTDOCSDIR}"" ; ${cmd} \
-		|| die "${cmd} failed."
-		cmd="cp applet.classes "${D}${MY_HTDOCSDIR}"" ; ${cmd} \
-		|| die "${cmd} failed."
-		cmd="cp -r build/classes/* "${D}${MY_HTDOCSDIR}"" ; ${cmd} \
-		|| die "${cmd} failed."
-		cmd="cp -r build/appletjars/* "${D}${MY_HTDOCSDIR}"" ; ${cmd} \
-		|| die "${cmd} failed."
-		cmd="cp "${FILESDIR}"/caffeine.xyz "${D}${MY_HTDOCSDIR}"" ; ${cmd} \
-		|| die "${cmd} failed."
-		cmd="cp "${FILESDIR}"/index.html "${D}${MY_HTDOCSDIR}"" ; ${cmd} \
-		|| die "${cmd} failed."
-
-		webapp_src_install || die "Failed running webapp_src_install"
-	fi
-}
-
-pkg_postinst() {
-
-	if ! use client-only ; then
-		webapp_pkg_postinst || die "webapp_pkg_postinst failed"
-	fi
-
-}
-
-pkg_prerm() {
-
-	if ! use client-only ; then
-		webapp_pkg_prerm || die "webapp_pkg_prerm failed"
-	fi
-
-}
diff --git a/sci-chemistry/jmol/jmol-12.0.34.ebuild b/sci-chemistry/jmol/jmol-12.0.34.ebuild
deleted file mode 100644
index aec92eed4..000000000
--- a/sci-chemistry/jmol/jmol-12.0.34.ebuild
+++ /dev/null
@@ -1,122 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=1
-WEBAPP_OPTIONAL="yes"
-
-inherit eutils java-pkg-2 java-ant-2 webapp
-
-MY_P=Jmol
-
-DESCRIPTION="Jmol is a java molecular viever for 3-D chemical structures."
-SRC_URI="mirror://sourceforge/${PN}/${MY_P}-${PV}-full.tar.gz"
-HOMEPAGE="http://jmol.sourceforge.net/"
-KEYWORDS="~amd64 ~x86"
-LICENSE="LGPL-2.1"
-
-IUSE="client-only vhosts"
-
-WEBAPP_MANUAL_SLOT="yes"
-SLOT="0"
-
-COMMON_DEP="dev-java/commons-cli:1
-	dev-java/itext:0
-	sci-libs/jmol-acme:0
-	sci-libs/vecmath-objectclub:0"
-
-RDEPEND=">=virtual/jre-1.4
-	${COMMON_DEP}"
-DEPEND=">=virtual/jdk-1.4
-	!client-only? ( ${WEBAPP_DEPEND} )
-	${COMMON_DEP}"
-
-pkg_setup() {
-
-	if ! use client-only ; then
-		webapp_pkg_setup || die "Failed to setup webapp"
-	fi
-
-	java-pkg-2_pkg_setup
-
-}
-
-src_unpack() {
-
-	unpack ${A}
-	cd "${S}"
-	epatch "${FILESDIR}"/${PV}/${PN}-nointl.patch
-	epatch "${FILESDIR}"/${PV}/${PN}-manifest.patch
-
-	mkdir "${S}"/selfSignedCertificate || die "Failed to create Cert directory."
-	cp "${FILESDIR}"/selfSignedCertificate.store "${S}"/selfSignedCertificate/ \
-		|| die "Failed to install Cert file."
-
-	rm -v "${S}"/*.jar "${S}"/plugin-jars/*.jar || die
-	cd "${S}/jars"
-
-# We still have to use netscape.jar on amd64 until a nice way to include plugin.jar comes along.
-	if use amd64; then
-		mv -v netscape.jar netscape.tempjar || die "Failed to move netscape.jar."
-		rm -v *.jar *.tar.gz || die "Failed to remove jars."
-		mv -v netscape.tempjar netscape.jar || die "Failed to move netscape.tempjar."
-	fi
-
-	java-pkg_jar-from vecmath-objectclub vecmath-objectclub.jar vecmath1.2-1.14.jar
-	java-pkg_jar-from itext iText.jar itext-1.4.5.jar
-	java-pkg_jar-from jmol-acme jmol-acme.jar Acme.jar
-	java-pkg_jar-from commons-cli-1 commons-cli.jar commons-cli-1.0.jar
-
-	mkdir -p "${S}/build/appjars" || die
-}
-
-src_compile() {
-	# prevent absorbing dep's classes
-	eant -Dlibjars.uptodate=true main
-}
-
-src_install() {
-
-	java-pkg_dojar build/Jmol.jar
-	dohtml -r  build/doc/* || die "Failed to install html docs."
-	dodoc *.txt doc/*license* || die "Failed to install licenses."
-
-	java-pkg_dolauncher ${PN} --main org.openscience.jmol.app.Jmol \
-		--java_args "-Xmx512m"
-
-	if ! use client-only ; then
-		webapp_src_preinst || die "Failed webapp_src_preinst."
-		cmd="cp Jmol.js build/Jmol.jar "${D}${MY_HTDOCSDIR}"" ; ${cmd} \
-		|| die "${cmd} failed."
-		cmd="cp build/JmolApplet*.jar "${D}${MY_HTDOCSDIR}"" ; ${cmd} \
-		|| die "${cmd} failed."
-		cmd="cp applet.classes "${D}${MY_HTDOCSDIR}"" ; ${cmd} \
-		|| die "${cmd} failed."
-		cmd="cp -r build/classes/* "${D}${MY_HTDOCSDIR}"" ; ${cmd} \
-		|| die "${cmd} failed."
-		cmd="cp -r build/appletjars/* "${D}${MY_HTDOCSDIR}"" ; ${cmd} \
-		|| die "${cmd} failed."
-		cmd="cp "${FILESDIR}"/caffeine.xyz "${D}${MY_HTDOCSDIR}"" ; ${cmd} \
-		|| die "${cmd} failed."
-		cmd="cp "${FILESDIR}"/index.html "${D}${MY_HTDOCSDIR}"" ; ${cmd} \
-		|| die "${cmd} failed."
-
-		webapp_src_install || die "Failed running webapp_src_install"
-	fi
-}
-
-pkg_postinst() {
-
-	if ! use client-only ; then
-		webapp_pkg_postinst || die "webapp_pkg_postinst failed"
-	fi
-
-}
-
-pkg_prerm() {
-
-	if ! use client-only ; then
-		webapp_pkg_prerm || die "webapp_pkg_prerm failed"
-	fi
-
-}
diff --git a/sci-chemistry/jmol/jmol-12.0.45.ebuild b/sci-chemistry/jmol/jmol-12.0.45-r1.ebuild
index 722c99d8e..722c99d8e 100644
--- a/sci-chemistry/jmol/jmol-12.0.45.ebuild
+++ b/sci-chemistry/jmol/jmol-12.0.45-r1.ebuild