Merge branch 'github-pr-103'

23 files changed, 751 insertions, 172 deletions

diff --git a/app-admin/ec2-api-tools/ec2-api-tools-1.6.7.2-r4.ebuild b/app-admin/ec2-api-tools/ec2-api-tools-1.6.7.2-r5.ebuild
index 954c81bb8dd7..ae4944da11f2 100644
--- a/app-admin/ec2-api-tools/ec2-api-tools-1.6.7.2-r4.ebuild
+++ b/app-admin/ec2-api-tools/ec2-api-tools-1.6.7.2-r5.ebuild
@@ -25,7 +25,7 @@ CDEPEND="
 	dev-java/jaxb:2
 	dev-java/jax-ws:2
 	dev-java/jsr173:0
-	dev-java/jdom:1.0
+	dev-java/jdom:0
 	dev-java/log4j:0
 	dev-java/wsdl4j:0
 	dev-java/xalan:0
@@ -70,7 +70,7 @@ src_install() {
 	dosym $(java-pkg_getjar jaxb{-2,-api.jar}) ${libs}/jaxb-api.jar
 	dosym $(java-pkg_getjar jaxb{-2,-impl.jar}) ${libs}/jaxb-impl.jar
 	dosym $(java-pkg_getjar jax-ws{-2,.jar}) ${libs}/jaxws-api.jar
-	dosym $(java-pkg_getjar jdom{-1.0,.jar}) ${libs}/jdom.jar
+	dosym $(java-pkg_getjar jdom{,.jar}) ${libs}/jdom.jar
 	dosym $(java-pkg_getjar log4j{,.jar}) ${libs}/log4j-1.2.14.jar
 	dosym $(java-pkg_getjar jsr173{,.jar}) ${libs}/stax2-api-3.0.1.jar
 	dosym $(java-pkg_getjar wsdl4j{,.jar}) ${libs}/wsdl4j.jar
diff --git a/app-office/hourglass/hourglass-0.7.2-r1.ebuild b/app-office/hourglass/hourglass-0.7.2-r1.ebuild
new file mode 100644
index 000000000000..eae8b3b97c4b
--- /dev/null
+++ b/app-office/hourglass/hourglass-0.7.2-r1.ebuild
@@ -0,0 +1,53 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+JAVA_PKG_IUSE="doc source"
+
+inherit java-pkg-2 java-ant-2 eutils
+
+DESCRIPTION="A PSP (personal software process) time tracking utility written in Java"
+HOMEPAGE="http://hourglass.wiki.sourceforge.net/"
+SRC_URI="mirror://sourceforge/${PN}/${P}-src.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+COMMON_DEPEND="dev-java/log4j
+		dev-java/jcommon:1.0
+		dev-java/jdom:0"
+
+DEPEND=">=virtual/jdk-1.5
+	dev-java/ant-core
+	${COMMON_DEPEND}"
+RDEPEND=">=virtual/jre-1.5
+	${COMMON_DEPEND}"
+
+S="${WORKDIR}/${P}-src"
+
+java_prepare() {
+	echo "jar.log4j=$(java-pkg_getjar log4j log4j.jar)" > conf/local.properties
+	echo "jar.jcommon=$(java-pkg_getjar jcommon:1.0 jcommon.jar)" >> conf/local.properties
+	echo "jar.jdom=$(java-pkg_getjar jdom jdom.jar)" >> conf/local.properties
+	echo "jar.ant=$(java-pkg_getjar --build-only ant-core ant.jar)" >> conf/local.properties
+}
+
+EANT_BUILD_TARGET="dist"
+EANT_DOC_TARGET="javadoc"
+
+src_install() {
+	java-pkg_dojar "dist/${P}/lib/${PN}.jar"
+
+	use doc && java-pkg_dojavadoc build/doc/api
+	use source && java-pkg_dosrc src/*
+
+	java-pkg_dolauncher "${PN}" \
+		--main "net.sourceforge.hourglass.swingui.Main"
+
+	make_desktop_entry "${PN}" "Hourglass" "appointment-new" "Office"
+
+	dodoc README ChangeLog AUTHORS
+}
diff --git a/dev-db/jxtray/jxtray-0.5-r5.ebuild b/dev-db/jxtray/jxtray-0.5-r5.ebuild
new file mode 100644
index 000000000000..35ee2300e012
--- /dev/null
+++ b/dev-db/jxtray/jxtray-0.5-r5.ebuild
@@ -0,0 +1,73 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+inherit java-pkg-2 java-ant-2
+
+DESCRIPTION="Java based Database Explorer"
+HOMEPAGE="http://jxtray.sourceforge.net"
+SRC_URI="mirror://sourceforge/jxtray/${PN}-src-${PV}.tgz"
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="doc firebird mssql mysql postgres"
+
+COMMON_DEP="
+	dev-java/jdom:0
+	>=dev-java/kunststoff-2.0.2:2.0
+	dev-java/poi:0
+	dev-java/sax:0
+	>=dev-java/xerces-2.7:2
+	dev-java/xml-commons:0
+	firebird? ( dev-java/jdbc-jaybird:0 )
+	mssql? ( >=dev-java/jtds-1.2:1.2 )
+	mysql? ( dev-java/jdbc-mysql:0 )
+	postgres? ( dev-java/jdbc-postgresql:0 )
+	!firebird? ( !mssql? ( !postgres? ( dev-java/jdbc-mysql:0 ) ) )"
+RDEPEND=">=virtual/jre-1.4
+	${COMMON_DEP}"
+DEPEND=">=virtual/jdk-1.4
+	${COMMON_DEP}"
+
+S="${WORKDIR}/${PN}-src-${PV}"
+
+src_unpack() {
+	unpack ${A}
+	cp "${FILESDIR}"/build.xml "${FILESDIR}"/default.properties "${S}"
+	local cp=""
+
+	cd "${S}"/lib
+	rm *.jar
+	cp="${cp}:$(java-pkg_getjars jdom)"
+	cp="${cp}:$(java-pkg_getjars xerces-2)"
+	cp="${cp}:$(java-pkg_getjars xml-commons)"
+	cp="${cp}:$(java-pkg_getjars sax)"
+	cp="${cp}:$(java-pkg_getjars poi)"
+
+	cd "${S}"/lib/lookandfeel
+	rm *.jar
+	cp="${cp}:$(java-pkg_getjars kunststoff-2.0)"
+
+	cd "${S}"/lib/drivers
+	rm *.jar
+	use firebird && cp="${cp}:$(java-pkg_getjars jdbc-jaybird)"
+	use mssql && cp="${cp}:$(java-pkg_getjars jtds-1.2)"
+	use mysql && cp="${cp}:$(java-pkg_getjars jdbc-mysql)"
+	use postgres && cp="${cp}:$(java-pkg_getjars jdbc-postgresql)"
+
+	echo "classpath=${cp}" > "${S}"/build.properties
+}
+
+src_compile() {
+	eant jar $(use_doc javadoc)
+}
+
+src_install() {
+	java-pkg_newjar dist/${P}.jar ${PN}.jar
+
+	java-pkg_dolauncher jxtray --main jxtray.Jxtray
+
+	dodoc CHANGELOG.txt README.txt
+	use doc && java-pkg_dojavadoc javadoc
+}
diff --git a/dev-java/commons-jxpath/commons-jxpath-1.3-r2.ebuild b/dev-java/commons-jxpath/commons-jxpath-1.3-r2.ebuild
new file mode 100644
index 000000000000..bcbf18f6faf7
--- /dev/null
+++ b/dev-java/commons-jxpath/commons-jxpath-1.3-r2.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+JAVA_PKG_IUSE="doc source test"
+
+inherit java-pkg-2 java-ant-2
+
+DESCRIPTION="Applies XPath expressions to graphs of objects of all kinds"
+HOMEPAGE="http://commons.apache.org/jxpath/"
+SRC_URI="mirror://apache/commons/jxpath/source/${P}-src.tar.gz"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~ppc64 ~x86 ~x86-fbsd"
+IUSE=""
+
+S="${WORKDIR}/${P}-src"
+
+CDEPEND="dev-java/commons-beanutils:1.7
+	java-virtuals/servlet-api:2.5
+	dev-java/jdom:0"
+RDEPEND=">=virtual/jre-1.6
+	${CDEPEND}"
+DEPEND=">=virtual/jdk-1.6
+	test? (
+		dev-java/commons-collections:0
+		dev-java/commons-logging:0
+	)
+	${CDEPEND}"
+
+src_unpack() {
+	unpack ${A}
+	cd "${S}"
+
+	mkdir -p "${S}/target/lib"
+	cd "${S}/target/lib"
+	java-pkg_jar-from commons-beanutils-1.7
+	java-pkg_jar-from servlet-api-2.5
+	java-pkg_jar-from jdom
+}
+
+src_prepare() {
+	# Don't automatically run tests
+	sed 's/depends="compile,test"/depends="compile"/' -i build.xml || die
+}
+
+src_test() {
+	# this one needs mockrunner #259027
+	rm src/test/org/apache/commons/jxpath/servlet/JXPathServletContextTest.java || die
+	java-pkg_jar-from --into target/lib \
+		commons-collections,commons-logging,junit
+	ANT_TASKS="ant-junit" eant test
+}
+
+src_install() {
+	java-pkg_dojar target/${PN}.jar
+	use doc && java-pkg_dojavadoc dist/docs/api
+	use source && java-pkg_dosrc src/java/*
+}
diff --git a/dev-java/jakarta-slide-webdavclient/jakarta-slide-webdavclient-2.1-r4.ebuild b/dev-java/jakarta-slide-webdavclient/jakarta-slide-webdavclient-2.1-r4.ebuild
new file mode 100644
index 000000000000..7808a130afc5
--- /dev/null
+++ b/dev-java/jakarta-slide-webdavclient/jakarta-slide-webdavclient-2.1-r4.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="2"
+JAVA_PKG_IUSE="doc source"
+
+inherit eutils java-pkg-2 java-ant-2
+
+MY_P="${PN}-src-${PV}"
+DESCRIPTION="A content repository"
+HOMEPAGE="http://jakarta.apache.org/slide/index.html"
+SRC_URI="http://archive.apache.org/dist/jakarta/slide/source/${MY_P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+RDEPEND=">=virtual/jre-1.4
+	dev-java/commons-httpclient:3
+	dev-java/jdom:0
+	dev-java/xml-im-exporter:0"
+DEPEND=">=virtual/jdk-1.4
+	${RDEPEND}"
+
+S="${WORKDIR}/${MY_P}"
+
+JAVA_ANT_REWRITE_CLASSPATH="true"
+
+src_prepare() {
+	epatch "${FILESDIR}/${P}-gentoo.patch"
+	rm -v lib/*.jar || die
+	java-pkg-2_src_prepare
+}
+
+EANT_GENTOO_CLASSPATH="jdom,commons-httpclient-3,xml-im-exporter"
+EANT_BUILD_TARGET="dist-clientlib"
+EANT_DOC_TARGET="javadoc-clientlib"
+
+src_install() {
+	java-pkg_newjar dist/lib/${P/client/lib}.jar ${PN/client/lib}.jar
+
+	dodoc README || die
+	use doc && java-pkg_dojavadoc build/clientlib/doc/clientjavadoc
+	use source && java-pkg_dosrc \
+		clientlib/src/java/* \
+		ant/src/java/* \
+		commandline/src/java/* \
+		connector/src/java/*
+}
diff --git a/dev-java/jaxen/jaxen-1.1.4.ebuild b/dev-java/jaxen/jaxen-1.1.4-r1.ebuild
index 2503e98ce30d..4c078bf24cab 100644
--- a/dev-java/jaxen/jaxen-1.1.4.ebuild
+++ b/dev-java/jaxen/jaxen-1.1.4-r1.ebuild
@@ -19,7 +19,7 @@ IUSE=""
 
 COMMON_DEP="
 	dev-java/dom4j:1
-	dev-java/jdom:1.0
+	dev-java/jdom:0
 	dev-java/xom:0"
 RDEPEND=">=virtual/jre-1.4
 	${COMMON_DEP}"
@@ -28,7 +28,7 @@ DEPEND=">=virtual/jdk-1.4
 	${COMMON_DEP}"
 
 JAVA_ANT_REWRITE_CLASSPATH="yes"
-EANT_GENTOO_CLASSPATH="dom4j-1,jdom-1.0,xom"
+EANT_GENTOO_CLASSPATH="dom4j-1,jdom,xom"
 EANT_TEST_EXTRA_ARGS="-DJunit.present=true"
 
 java_prepare() {
diff --git a/dev-java/jdom/jdom-1.1.3.ebuild b/dev-java/jdom/jdom-1.1.3.ebuild
index dbf6f1e135c7..5403ba96d4f1 100644
--- a/dev-java/jdom/jdom-1.1.3.ebuild
+++ b/dev-java/jdom/jdom-1.1.3.ebuild
@@ -12,7 +12,7 @@ SRC_URI="http://www.jdom.org/dist/binary/archive/${P}.tar.gz"
 HOMEPAGE="http://www.jdom.org"
 LICENSE="JDOM"
 SLOT="0"
-KEYWORDS="amd64 ppc ppc64 x86"
+KEYWORDS="amd64 ~arm ppc ppc64 x86"
 COMMON_DEP="dev-java/saxpath
 		>=dev-java/xerces-2.7"
 RDEPEND=">=virtual/jre-1.6"
diff --git a/dev-java/junit-addons/junit-addons-1.4.ebuild b/dev-java/junit-addons/junit-addons-1.4-r1.ebuild
index c0b8ddc23679..4df5fa14ad18 100644
--- a/dev-java/junit-addons/junit-addons-1.4.ebuild
+++ b/dev-java/junit-addons/junit-addons-1.4-r1.ebuild
@@ -1,7 +1,9 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
+EAPI=5
+
 JAVA_PKG_IUSE="doc source"
 
 inherit java-pkg-2 java-ant-2
@@ -15,10 +17,10 @@ SLOT="0"
 KEYWORDS="~amd64 ~x86 ~x86-linux ~x86-macos"
 
 COMMON_DEP="
-	=dev-java/junit-3.8*
-	dev-java/ant-core
-	~dev-java/jdom-1.0
-	=dev-java/jaxen-1.1*
+	dev-java/junit:0
+	dev-java/ant-core:0
+	dev-java/jdom:0
+	dev-java/jaxen:1.1
 	"
 
 RDEPEND=">=virtual/jre-1.4
@@ -27,9 +29,7 @@ DEPEND=">=virtual/jdk-1.4
 		app-arch/unzip
 		${COMMON_DEP}"
 
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
+java_prepare() {
 	unpack ./src.jar
 	rm -v *.jar || die
 	# Not included so taken from cvs
@@ -41,7 +41,7 @@ _eant() {
 	eant \
 		-Djunit.jar="$(java-pkg_getjar junit junit.jar)" \
 		-Dant.jar="$(java-pkg_getjar ant-core ant.jar)" \
-		-Djdom.jar="$(java-pkg_getjar jdom-1.0 jdom.jar)" \
+		-Djdom.jar="$(java-pkg_getjar jdom jdom.jar)" \
 		-Djaxen.jar="$(java-pkg_getjar jaxen-1.1 jaxen.jar)" \
 		"${@}"
 }
diff --git a/dev-java/rome/rome-0.9-r1.ebuild b/dev-java/rome/rome-0.9-r1.ebuild
new file mode 100644
index 000000000000..30702d286ee8
--- /dev/null
+++ b/dev-java/rome/rome-0.9-r1.ebuild
@@ -0,0 +1,48 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+JAVA_PKG_IUSE="doc source test"
+
+inherit java-pkg-2 java-ant-2
+
+DESCRIPTION="Open source Atom/RSS Java utilities that make it easy to work in Java with most syndication formats"
+HOMEPAGE="https://java.net/projects/rome"
+SRC_URI="https://rome.dev.java.net/source/browse/*checkout*/rome/www/dist/${P}-src.zip"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~x86-fbsd"
+IUSE=""
+
+COMMON_DEPEND="dev-java/jdom:0"
+DEPEND=">=virtual/jdk-1.4
+	app-arch/unzip
+	test? ( dev-java/ant-junit:0 )
+	${COMMON_DEPEND}"
+RDEPEND=">=virtual/jre-1.4
+	${COMMON_DEPEND}"
+
+JAVA_ANT_REWRITE_CLASSPATH="true"
+EANT_GENTOO_CLASSPATH="jdom"
+
+java_prepare() {
+	# Patch build.xml so the tests pass
+	epatch "${FILESDIR}/${P}-build.xml-test-upstream.patch"
+
+	# Keep Ant happy.
+	mkdir -p target/lib || die
+}
+
+src_install() {
+	java-pkg_newjar target/${P}.jar
+
+	use doc && java-pkg_dojavadoc dist/docs/api
+	use source && java-pkg_dosrc src/java/*
+}
+
+src_test() {
+	java-pkg-2_src_test
+}
diff --git a/dev-java/saxon/saxon-6.5.5-r1.ebuild b/dev-java/saxon/saxon-6.5.5-r1.ebuild
new file mode 100644
index 000000000000..7b2871efca79
--- /dev/null
+++ b/dev-java/saxon/saxon-6.5.5-r1.ebuild
@@ -0,0 +1,60 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+JAVA_PKG_IUSE="doc examples source"
+inherit java-pkg-2 java-ant-2 eutils versionator
+
+MY_P="${PN}$(replace_all_version_separators -)"
+DESCRIPTION="A collection of tools for processing XML documents: XSLT processor, XSL library, parser"
+SRC_URI="mirror://sourceforge/${PN}/${MY_P}.zip"
+HOMEPAGE="http://saxon.sourceforge.net/"
+
+LICENSE="MPL-1.1"
+SLOT="6.5"
+KEYWORDS="~amd64 ~ppc ~x86"
+IUSE=""
+
+COMMON_DEP="dev-java/jdom:0"
+
+RDEPEND=">=virtual/jre-1.4
+	${COMMON_DEP}"
+
+DEPEND=">=virtual/jdk-1.4
+	app-arch/unzip
+	${COMMON_DEP}"
+
+S="${WORKDIR}"
+
+src_unpack() {
+	unpack ${A}
+
+	unzip -qq source.zip -d src || die "failed to unpack"
+
+	cp "${FILESDIR}/build-${PV}.xml" build.xml || die
+
+	rm -v *.jar || die
+	rm -rf doc/api || die
+	rm samples/java/*.class || die
+	mkdir lib && cd lib
+	java-pkg_jar-from jdom
+}
+
+src_compile() {
+	java-pkg_filter-compiler jikes
+
+	eant -Dproject.name=${PN} jar $(use_doc)
+}
+
+src_install() {
+	java-pkg_dojar dist/${PN}.jar
+
+	if use doc; then
+		java-pkg_dojavadoc dist/doc/api
+		dohtml -r doc/*
+	fi
+	use examples && java-pkg_doexamples samples
+	use source && java-pkg_dosrc src/*
+}
diff --git a/dev-java/saxon/saxon-8.4b-r4.ebuild b/dev-java/saxon/saxon-8.4b-r4.ebuild
new file mode 100644
index 000000000000..20bb1ba046e5
--- /dev/null
+++ b/dev-java/saxon/saxon-8.4b-r4.ebuild
@@ -0,0 +1,68 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+JAVA_PKG_IUSE="doc examples source"
+
+inherit java-pkg-2 eutils java-ant-2
+
+DESCRIPTION="A collection of tools for processing XML documents: XSLT processor, XSL library, parser"
+MyPV=${PV%b}
+SRC_URI="mirror://sourceforge/saxon/saxonb${MyPV/./-}.zip"
+HOMEPAGE="http://saxon.sourceforge.net/"
+
+LICENSE="MPL-1.1"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86"
+IUSE=""
+
+COMMON_DEP="
+	dev-java/xom
+	dev-java/jdom:0
+	=dev-java/xml-commons-external-1.3*"
+RDEPEND=">=virtual/jre-1.4
+	${COMMON_DEP}"
+
+DEPEND=">=virtual/jdk-1.4
+	app-arch/unzip
+	${COMMON_DEP}"
+
+S=${WORKDIR}
+
+src_unpack() {
+	unpack ${A}
+
+	unpack ./source.zip
+	mkdir src
+	mv net src
+
+	epatch "${FILESDIR}/${P}-jikes.patch"
+
+	cp -i "${FILESDIR}/build-${PV}.xml" build.xml || die
+
+	rm -v *.jar || die
+	rm samples/java/*.class || die
+
+	mkdir lib && cd lib
+	java-pkg_jar-from jdom
+	java-pkg_jar-from xom
+	# Is not needed with 1.5 but gets pulled in by deps any way
+	# without this emerging with sun-jdk-1.4 fails with
+	# JAVA_PKG_STRICT
+	java-pkg_jar-from xml-commons-external-1.3
+}
+
+src_install() {
+	java-pkg_dojar dist/*.jar
+
+	# the jar is named saxon8 and and helps if new slots come along
+	java-pkg_dolauncher ${PN}8 --main net.sf.saxon.Transform
+	if use doc; then
+		java-pkg_dojavadoc dist/doc/api doc/*
+		java-pkg_dohtml doc/*
+	fi
+	use examples && java-pkg_doexamples samples
+	use source && java-pkg_dosrc src/*
+}
diff --git a/dev-java/saxon/saxon-9.2.0.6-r1.ebuild b/dev-java/saxon/saxon-9.2.0.6-r1.ebuild
new file mode 100644
index 000000000000..0694e74acd6e
--- /dev/null
+++ b/dev-java/saxon/saxon-9.2.0.6-r1.ebuild
@@ -0,0 +1,98 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="3"
+
+JAVA_PKG_IUSE="doc source"
+
+inherit versionator java-pkg-2 java-ant-2
+
+MY_PV="$(replace_all_version_separators -)"
+
+DESCRIPTION="A XSLT and XQuery Processor"
+HOMEPAGE="http://saxon.sourceforge.net/"
+SRC_URI="mirror://sourceforge/${PN}/${PN}he${MY_PV}source.zip"
+
+LICENSE="MPL-1.0"
+SLOT="9"
+KEYWORDS="~amd64 ~arm ~ppc ~ppc64 ~x86 ~x86-fbsd"
+
+IUSE=""
+
+# virtual/jdk slot for external javadoc
+JDK_VER="6"
+# dev-java/jdom slot for external javadoc
+JDOM_VER="0"
+# dev-java/dom4j slot
+DOM4J_VER="1"
+
+CDEPEND="dev-java/ant-core
+	dev-java/dom4j:${DOM4J_VER}
+	dev-java/jdom:${JDOM_VER}
+	dev-java/xom"
+RDEPEND=">=virtual/jre-1.${JDK_VER}
+	${CDEPEND}"
+DEPEND=">=virtual/jdk-1.${JDK_VER}
+	app-arch/unzip
+	${CDEPEND}"
+
+S="${WORKDIR}"
+
+# prepare eclass variables
+JAVA_ANT_REWRITE_CLASSPATH="yes"
+JAVA_ANT_CLASSPATH_TAGS="javac javadoc"
+
+src_unpack() {
+	unpack ${A}
+
+	### fedora-inspired remove
+
+	# deadNET
+	rm -rv net/sf/saxon/dotnet
+
+	# Depends on XQJ (javax.xml.xquery)
+	rm -rv net/sf/saxon/xqj
+
+	# This requires a EE edition feature (com.saxonica.xsltextn)
+	rm -v net/sf/saxon/option/sql/SQLElementFactory.java
+}
+
+java_prepare() {
+	# <major>.<minor> version
+	local version="$(get_version_component_range 1-2)"
+
+	# generate build.xml with external javadoc links
+	sed -e "s:@JDK@:${JDK_VER}:" \
+		-e "s:@JDOM@:${JDOM_VER}:" \
+		< "${FILESDIR}/${version}-build.xml" \
+		> "${S}/build.xml" \
+		|| die "build.xml generation failed!"
+
+	# prepare creates the dir for properties
+	eant prepare
+
+	# properties
+	cp -v \
+		"${FILESDIR}/${version}-edition.properties" \
+		"${S}/build/classes/edition.properties"
+}
+
+src_compile() {
+	local gcp="$(java-pkg_getjars dom4j-${DOM4J_VER},jdom,xom)"
+	gcp="${gcp}:$(java-pkg_getjars --build-only ant-core)"
+	eant -Dgentoo.classpath="${gcp}" jar $(use_doc)
+}
+
+src_install() {
+	java-pkg_dojar build/lib/${PN}.jar
+
+	java-pkg_dolauncher ${PN}${SLOT}-transform --main net.sf.saxon.Transform
+	java-pkg_dolauncher ${PN}${SLOT}-query --main net.sf.saxon.Query
+
+	java-pkg_register-ant-task
+
+	use doc && java-pkg_dojavadoc build/api
+
+	use source && java-pkg_dosrc src
+}
diff --git a/dev-java/velocity/velocity-1.7-r1.ebuild b/dev-java/velocity/velocity-1.7-r1.ebuild
new file mode 100644
index 000000000000..56d72eadf8f0
--- /dev/null
+++ b/dev-java/velocity/velocity-1.7-r1.ebuild
@@ -0,0 +1,87 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+JAVA_PKG_IUSE="examples doc source"
+
+inherit java-pkg-2 java-ant-2 eutils
+
+DESCRIPTION="A Java-based template engine for easy creation/rendering of documents that format and present data"
+HOMEPAGE="http://velocity.apache.org"
+SRC_URI="mirror://apache/${PN}/engine/${PV}/${P}.tar.gz"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~x86-fbsd"
+IUSE="test"
+
+CDEPEND="
+	dev-java/commons-collections:0
+	dev-java/commons-lang:2.1
+	dev-java/commons-logging:0
+	dev-java/jdom:0
+	dev-java/log4j:0
+	dev-java/avalon-logkit:2.0
+	dev-java/jakarta-oro:2.0
+	java-virtuals/servlet-api:2.3
+	dev-java/werken-xpath:0
+	dev-java/ant-core:0
+"
+DEPEND="${CDEPEND}
+	>=virtual/jdk-1.4
+	test? (
+		dev-java/ant-junit:0
+		dev-java/ant-antlr:0
+		dev-db/hsqldb:0
+	)
+"
+RDEPEND="${CDEPEND}
+	>=virtual/jre-1.4"
+
+JAVA_PKG_FILTER_COMPILER="jikes"
+JAVA_ANT_REWRITE_CLASSPATH="yes"
+
+EANT_GENTOO_CLASSPATH="
+	commons-collections
+	commons-lang-2.1
+	commons-logging
+	jdom
+	log4j
+	avalon-logkit-2.0
+	jakarta-oro-2.0
+	servlet-api-2.3
+	werken-xpath
+	ant-core
+"
+
+# One test fails. see #219668
+RESTRICT="test"
+
+java_prepare() {
+	rm -v *.jar lib/test/*.jar lib/*.jar || die
+}
+
+src_compile () {
+	cd "${S}"/build
+	eant jar -Dskip-download=true #prebuilt javadocs
+}
+
+src_test() {
+	mkdir -p bin/test-lib || die
+	cd bin/test-lib || die
+	java-pkg_jar-from junit,hsqldb
+	java-pkg_jar-from --virtual servlet-api-2.3
+	cd "${S}"/build
+	ANT_TASKS="ant-junit ant-antlr" eant test -Dskip-download=true
+}
+
+src_install () {
+	java-pkg_newjar bin/*.jar
+
+	dodoc NOTICE README.txt
+	# has other stuff besides api too
+	use doc && java-pkg_dohtml -r docs/*
+	use examples && java-pkg_doexamples examples
+	use source && java-pkg_dosrc src/java/*
+}
diff --git a/dev-java/werken-xpath/werken-xpath-0.9.4_beta-r3.ebuild b/dev-java/werken-xpath/werken-xpath-0.9.4_beta-r3.ebuild
new file mode 100644
index 000000000000..709ed3e0219d
--- /dev/null
+++ b/dev-java/werken-xpath/werken-xpath-0.9.4_beta-r3.ebuild
@@ -0,0 +1,60 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+JAVA_PKG_IUSE="doc source"
+WANT_ANT_TASKS="ant-antlr"
+
+inherit java-pkg-2 java-ant-2 eutils versionator
+
+MY_PN=${PN/-/.}
+MY_PV=$(replace_version_separator 3 '-')
+MY_P=${MY_PN}-${MY_PV}
+
+DESCRIPTION="W3C XPath-Rec implementation for DOM4J"
+HOMEPAGE="http://sourceforge.net/projects/werken-xpath/"
+SRC_URI="mirror://gentoo/${MY_P}-src.tar.gz"
+# This tarball was acquired from jpackage's src rpm of the package by the same name
+
+LICENSE="JDOM"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~x86-fbsd"
+
+COMMON_DEP="
+	dev-java/jdom:0
+	>=dev-java/antlr-2.7.7:0[java]"
+DEPEND=">=virtual/jdk-1.4
+	${COMMON_DEP}"
+RDEPEND=">=virtual/jre-1.4
+	${COMMON_DEP}"
+
+S=${WORKDIR}/${MY_PN}
+
+EANT_BUILD_TARGET="package"
+JAVA_ANT_REWRITE_CLASSPATH="yes"
+EANT_GENTOO_CLASSPATH="antlr,jdom"
+
+java_prepare() {
+	# Courtesy of JPackages :)
+	epatch "${FILESDIR}"/${P}-jpp-compile.patch
+	epatch "${FILESDIR}"/${P}-jpp-jdom.patch
+	epatch "${FILESDIR}"/${P}-jpp-tests.patch
+	epatch "${FILESDIR}"/${P}-gentoo.patch
+
+	# API updates to support jdom:1.0
+	epatch "${FILESDIR}"/${P}-jdom-1.0.patch
+
+	cd "${S}"/lib
+	# In here we have ant starter scripts
+	rm -fr bin
+	rm -f *.jar
+}
+
+src_install() {
+	java-pkg_newjar build/${MY_PN}.jar
+
+	dodoc README TODO LIMITATIONS
+	use doc && java-pkg_dojavadoc build/apidocs
+	use source && java-pkg_dosrc src/*
+}
diff --git a/dev-java/xstream/xstream-1.3.1-r4.ebuild b/dev-java/xstream/xstream-1.3.1-r4.ebuild
index bd8cd61917a1..e0f82b3bb844 100644
--- a/dev-java/xstream/xstream-1.3.1-r4.ebuild
+++ b/dev-java/xstream/xstream-1.3.1-r4.ebuild
@@ -24,7 +24,7 @@ RESTRICT="test"
 
 CDEPEND="dev-java/cglib:3
 	dev-java/dom4j:1
-	dev-java/jdom:1.0
+	dev-java/jdom:0
 	dev-java/joda-time:0
 	dev-java/xom:0
 	dev-java/xpp3:0
@@ -41,7 +41,7 @@ DEPEND=">=virtual/jdk-1.6
 S="${WORKDIR}/${P}/${PN}"
 
 JAVA_ANT_REWRITE_CLASSPATH="true"
-EANT_GENTOO_CLASSPATH="xpp3,jdom-1.0,xom,dom4j-1,joda-time,cglib-3,xml-commons-external-1.3,jettison"
+EANT_GENTOO_CLASSPATH="xpp3,jdom,xom,dom4j-1,joda-time,cglib-3,xml-commons-external-1.3,jettison"
 EANT_BUILD_TARGET="benchmark:compile jar"
 EANT_EXTRA_ARGS="-Dversion=${PV} -Djunit.haltonfailure=true"
 
diff --git a/dev-vcs/statcvs/statcvs-0.5.0-r1.ebuild b/dev-vcs/statcvs/statcvs-0.5.0-r1.ebuild
new file mode 100644
index 000000000000..5dbc8fa056f7
--- /dev/null
+++ b/dev-vcs/statcvs/statcvs-0.5.0-r1.ebuild
@@ -0,0 +1,68 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=2
+JAVA_PKG_IUSE="doc source test"
+
+inherit eutils java-pkg-2 java-ant-2
+
+DESCRIPTION="StatCVS generates HTML reports from CVS repository logs"
+HOMEPAGE="http://statcvs.sourceforge.net/"
+SRC_URI="mirror://sourceforge/${PN}/${P}-source.zip"
+LICENSE="LGPL-2.1"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+COMMON_DEPEND="
+	dev-java/jcommon:1.0
+	>=dev-java/jfreechart-1.0.11:1.0
+	dev-java/jdom:0
+	dev-java/ant-core:0"
+
+DEPEND=">=virtual/jdk-1.4
+	app-arch/unzip
+	test? ( dev-java/ant-junit:0 )
+	${COMMON_DEPEND}"
+
+RDEPEND=">=virtual/jre-1.4
+	dev-vcs/cvs
+	dev-java/jtreemap:0
+	${COMMON_DEPEND}"
+
+EANT_BUILD_TARGET="compile copyfiles jar"
+
+java_prepare() {
+	epatch "${FILESDIR}"/${P}-build.xml.patch
+	epatch "${FILESDIR}"/${PN}-0.4.0-external-jtreemap.patch
+
+	einfo "Removing bundled jars."
+	find . -name "*.jar" -print -delete
+
+	cd "${S}"/lib || die
+	java-pkg_jar-from jcommon-1.0 jcommon.jar jcommon-1.0.6.jar
+	java-pkg_jar-from jfreechart-1.0 jfreechart.jar jfreechart-1.0.3.jar
+	java-pkg_jar-from jdom jdom.jar
+	java-pkg_jar-from ant-core ant.jar
+}
+
+src_install() {
+	java-pkg_dojar dist/${PN}.jar
+	java-pkg_dolauncher ${PN} --main net.sf.statcvs.Main
+
+	use doc && java-pkg_dohtml -r doc/*
+	use source && java-pkg_dosrc src/net
+}
+
+src_test() {
+	java-pkg_jar-from --into lib junit
+	ANT_TASKS="ant-junit" eant test
+}
+
+pkg_postinst() {
+	elog "For instructions on how to use StatCVS see"
+	elog "http://statcvs.sourceforge.net/manual/"
+	elog "You need to regenerate statistics"
+	elog "if you update dev-java/jtreemap"
+}
diff --git a/media-video/google2srt/Manifest b/media-video/google2srt/Manifest
index dbbdcf598c66..feca2fc280b2 100644
--- a/media-video/google2srt/Manifest
+++ b/media-video/google2srt/Manifest
@@ -1,3 +1,2 @@
-DIST Google2SRT-0.5.3.zip 334238 SHA256 bcc43a2b50f82373122382adf0e17b0bd3bb0170fd58d74c4582b52faa73a7de SHA512 948aa0085750db96d16da8a693c16e14c2546aebf305544c13984c043671c81e7e94e03e4659227a9be9edf3dc25d78968c0e6d7e6dbb81d925aa3aa0fedb331 WHIRLPOOL 5cd701ea8c3d93791c1199cfad990c697023ddb9ad8308ddd8ec0e14d50661aa108fec7cd82b9654adbc1a777ca36e8f42c20bb133f704676a55d16bd3055fff
 DIST Google2SRT-0.5.6.zip 355167 SHA256 9f021954ff2ed3b386211a839784ae213403981f53068c51a9d2733865b249bb SHA512 edb7b1ee4440f4962220557c794090edb9b3647a64deb70c19170bb4af3edbb5abc93ddd6061badf458c6cd92c17024b91bbdfa95bb1b366d1092b659db08094 WHIRLPOOL 63b120cf28019c0c39132c99e3877ec264b5396a15003c1a235fd296aab4b178048a45a406c5697adef4ac45ab0ea5ac845a4c4665de2f0fce8b4a360ccea2c7
 DIST google2srt-icon.png 1848 SHA256 d832d20322e79ad74950e0bd2168f402d18f4de2ffeff0ba7d573092b0d6e588 SHA512 051d8ffe8488e2521cdfbfd045d6b5159a18619e12dc1216b1687514cf3f1cebdf2167af372c2ec46d3886412350f5872e8a8c245fee341a30fec51615b5140f WHIRLPOOL 5a9a0c9388a0e2d8e76d87a4ff0446b83399cb5c8ca5d8718982356431a2abc9461517363590cad8dca534e75c172aecc841956392bc01b94ec965bbcb15f98b
diff --git a/media-video/google2srt/google2srt-0.5.3.ebuild b/media-video/google2srt/google2srt-0.5.3.ebuild
deleted file mode 100644
index 6bbf61cc8b95..000000000000
--- a/media-video/google2srt/google2srt-0.5.3.ebuild
+++ /dev/null
@@ -1,64 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI="2"
-
-JAVA_PKG_IUSE="doc source"
-
-inherit eutils java-pkg-2 java-ant-2
-
-MY_PN="Google2SRT"
-MY_P="${MY_PN}-${PV}"
-MAINCLASS="GUI"
-
-DESCRIPTION="Convert subtitles from Google Video and YouTube to SubRip (.srt) format"
-HOMEPAGE="http://google2srt.sourceforge.net/en/"
-SRC_URI="mirror://sourceforge/${PN}/${MY_P}.zip
-	http://sbriesen.de/gentoo/distfiles/google2srt-icon.png"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="html"
-
-COMMON_DEP="dev-java/jdom:1.0"
-
-RDEPEND=">=virtual/jre-1.6
-	${COMMON_DEP}"
-
-DEPEND=">=virtual/jdk-1.6
-	${COMMON_DEP}"
-
-S="${WORKDIR}/${MY_P}"
-
-java_prepare() {
-	# copy build.xml
-	cp -f "${FILESDIR}/build.xml" build.xml || die
-
-	# move resources
-	mkdir -p "resources"
-	mv -f src/*.{jpg,properties} "resources/"
-
-	# update library packages
-	cd lib
-	rm -f jdom.jar ../${MY_PN}.jar || die
-	java-pkg_jar-from jdom-1.0
-	java-pkg_ensure-no-bundled-jars
-}
-
-src_compile() {
-	eant build $(use_doc)
-}
-
-src_install() {
-	java-pkg_dojar dist/${MY_PN}.jar
-	java-pkg_dolauncher ${MY_PN} --main ${MAINCLASS} --java_args -Xmx256m
-	newicon "${DISTDIR}/${PN}-icon.png" "${MY_PN}.png"
-	make_desktop_entry ${MY_PN} ${MY_PN} ${MY_PN}
-	use doc && java-pkg_dojavadoc apidocs
-	use source && java-pkg_dosrc src
-	use html && dohtml -r doc
-	newdoc Changelog.txt ChangeLog
-	newdoc README.TXT README
-}
diff --git a/media-video/google2srt/google2srt-0.5.6.ebuild b/media-video/google2srt/google2srt-0.5.6-r1.ebuild
index ce5e84064429..29ba0349f109 100644
--- a/media-video/google2srt/google2srt-0.5.6.ebuild
+++ b/media-video/google2srt/google2srt-0.5.6-r1.ebuild
@@ -22,7 +22,7 @@ SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE="html"
 
-COMMON_DEP="dev-java/jdom:1.0"
+COMMON_DEP="dev-java/jdom:0"
 
 RDEPEND=">=virtual/jre-1.6
 	${COMMON_DEP}"
@@ -43,7 +43,7 @@ java_prepare() {
 	# update library packages
 	cd lib
 	rm -f jdom.jar ../${MY_PN}.jar || die
-	java-pkg_jar-from jdom-1.0
+	java-pkg_jar-from jdom
 	java-pkg_ensure-no-bundled-jars
 }
 
diff --git a/sci-biology/beast-mcmc/Manifest b/sci-biology/beast-mcmc/Manifest
index 7fd843d7d423..56293f2fdd27 100644
--- a/sci-biology/beast-mcmc/Manifest
+++ b/sci-biology/beast-mcmc/Manifest
@@ -1,2 +1 @@
-DIST beast-mcmc-1.5.2.tar.bz2 38834702 SHA256 f7312c6a7a14f6b32e9701a6386ff87728574460b7861880aa2cb87290756ea1 SHA512 8549db6cb49d64eb3a97fa6478bdbabfecd44ccc6236c474a1961ec5d6fc8326072fb961035df70982a9f1c08a36572529a07b88e2d33a43fa0fd5c07df3a414 WHIRLPOOL 595f606640daa32c79373c9003ddbc1f80dcbbf01e9e9c18191328b80eb50b45ac70032027dd1efb0e256d78b88bfe1742151a16f6f333938099943a7b2cd16a
 DIST beast-mcmc-1.7.5.tar.xz 40516312 SHA256 905248cbf07513a0d11375656391d86e310d28f07b6fe78de6b9768eb2548f4f SHA512 9b2ab98fdc5a173e8d9fc74d27cdfd8105e9685fdcbe69a373666e77b6865b74fdd87dfa404fc4ab5bea927728d5b6b35fabd5e376a66e5f014e978952797937 WHIRLPOOL 2daded22cfd59b3b44908ce27f4ef61178f5d174de02080a7e94ba311462f482e381556d4b81bc053e33e1c4bb193d172f2c23f331659b3548f7900d3fc297d5
diff --git a/sci-biology/beast-mcmc/beast-mcmc-1.5.2.ebuild b/sci-biology/beast-mcmc/beast-mcmc-1.5.2.ebuild
deleted file mode 100644
index e3566919c375..000000000000
--- a/sci-biology/beast-mcmc/beast-mcmc-1.5.2.ebuild
+++ /dev/null
@@ -1,82 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI="2"
-
-ESVN_REPO_URI="https://beast-mcmc.googlecode.com/svn/trunk/"
-
-WANT_ANT_TASKS="ant-junit4"
-EANT_GENTOO_CLASSPATH="colt,jdom-1.0,itext,junit-4,jebl,matrix-toolkits-java,commons-math-2,jdom-jaxen-1.0"
-JAVA_ANT_REWRITE_CLASSPATH="true"
-JAVA_ANT_ENCODING="latin1"
-JAVA_PKG_BSFIX_NAME="build.xml build_BEAST_MCMC.xml build_coalsim.xml build_development.xml build_pathogen.xml build_release.xml build_treestat.xml build_vcs.xml"
-
-#inherit java-pkg-2 java-ant-2 eutils subversion
-inherit java-pkg-2 java-ant-2 eutils
-
-DESCRIPTION="Bayesian MCMC of Evolution & Phylogenetics using Molecular Sequences"
-HOMEPAGE="https://github.com/beast-dev/beast-mcmc"
-#SRC_URI=""
-SRC_URI="mirror://gentoo/${P}.tar.bz2"
-
-LICENSE="LGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-# TODO: sys-cluster/mpijava
-COMMON_DEPS="dev-java/colt:0
-	dev-java/jdom:1.0
-	dev-java/itext:0
-	dev-java/junit:4
-	dev-java/jebl:0
-	dev-java/matrix-toolkits-java
-	dev-java/commons-math:2
-	dev-java/jdom-jaxen:1.0"
-DEPEND=">=virtual/jdk-1.5
-	${COMMON_DEPS}"
-RDEPEND=">=virtual/jre-1.5
-	${COMMON_DEPS}"
-
-S="${WORKDIR}/beast_release_${PV//./_}"
-
-src_prepare() {
-	sed -i '/BEAST_LIB/ s|$BEAST|/usr/share/beast|' "${S}"/scripts/* || die
-	cd lib
-	rm -v colt.jar junit-*.jar itext-*.jar jdom.jar jebl.jar mtj.jar commons-math-*.jar || die
-	java-pkg_jar-from jdom-1.0
-	java-pkg_jar-from colt
-	java-pkg_jar-from itext
-	java-pkg_jar-from jebl
-	java-pkg_jar-from matrix-toolkits-java
-	java-pkg_jar-from commons-math-1
-	java-pkg-2_src_prepare
-}
-
-src_compile() {
-	eant dist_all_BEAST -f build_BEAST_MCMC.xml \
-		-Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) || die
-	eant dist -f build_pathogen.xml \
-		-Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) || die
-}
-
-src_install() {
-	java-pkg_dojar build/dist/*.jar dist/*.jar
-
-	java-pkg_dolauncher beauti --jar beauti.jar --java_args '-Xms64m -Xmx256m'
-#	java-pkg_dolauncher beauti --main dr.app.beauti.BeautiApp --java_args '-Xms64m -Xmx256m'
-	java-pkg_dolauncher beast --main dr.app.beast.BeastMain --java_args '-Xms64m -Xmx256m'
-	java-pkg_dolauncher loganalyser --main dr.app.tools.LogAnalyser --java_args '-Xms64m -Xmx256m'
-	java-pkg_dolauncher logcombiner --main dr.app.tools.LogCombiner --java_args '-Xms64m -Xmx256m'
-	java-pkg_dolauncher treeannotator --main dr.app.tools.TreeAnnotator --java_args '-Xms64m -Xmx256m'
-
-	insinto /usr/share/${PN}
-	doins -r examples || die
-	dodoc NOTIFY doc/*.pdf
-}
-
-src_test() {
-	eant junit -f build_BEAST_MCMC.xml \
-		-Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) || die
-}
diff --git a/sci-biology/beast-mcmc/beast-mcmc-1.7.5.ebuild b/sci-biology/beast-mcmc/beast-mcmc-1.7.5-r1.ebuild
index 5a66f595593c..8e59912e7175 100644
--- a/sci-biology/beast-mcmc/beast-mcmc-1.7.5.ebuild
+++ b/sci-biology/beast-mcmc/beast-mcmc-1.7.5-r1.ebuild
@@ -7,7 +7,7 @@ EAPI=5
 ESVN_REPO_URI="https://beast-mcmc.googlecode.com/svn/trunk/"
 
 WANT_ANT_TASKS="ant-junit4"
-EANT_GENTOO_CLASSPATH="colt,jdom-1.0,itext,junit-4,jebl,matrix-toolkits-java,commons-math-2,jdom-jaxen-1.0"
+EANT_GENTOO_CLASSPATH="colt,jdom,itext,junit-4,jebl,matrix-toolkits-java,commons-math-2,jdom-jaxen-1.0"
 JAVA_ANT_REWRITE_CLASSPATH="true"
 JAVA_ANT_ENCODING="latin1"
 JAVA_PKG_BSFIX_NAME="build.xml build_BEAST_MCMC.xml build_coalsim.xml build_development.xml build_pathogen.xml build_release.xml build_treestat.xml build_vcs.xml"
@@ -30,7 +30,7 @@ IUSE=""
 # TODO: sys-cluster/mpijava
 COMMON_DEPS="
 	dev-java/colt:0
-	dev-java/jdom:1.0
+	dev-java/jdom:0
 	dev-java/itext:0
 	dev-java/junit:4
 	dev-java/jebl:0
@@ -49,7 +49,7 @@ src_prepare() {
 	cd lib
 	rm -v colt.jar junit-*.jar itext-*.jar jdom.jar mtj.jar commons-math-*.jar || die
 	#rm -v colt.jar junit-*.jar itext-*.jar jdom.jar jebl.jar mtj.jar commons-math-*.jar || die
-	java-pkg_jar-from jdom-1.0
+	java-pkg_jar-from jdom
 	java-pkg_jar-from colt
 	java-pkg_jar-from itext
 #	java-pkg_jar-from jebl
diff --git a/sci-biology/beast-mcmc/beast-mcmc-9999.ebuild b/sci-biology/beast-mcmc/beast-mcmc-9999.ebuild
index 768799ce2195..7bb1f0faa1b3 100644
--- a/sci-biology/beast-mcmc/beast-mcmc-9999.ebuild
+++ b/sci-biology/beast-mcmc/beast-mcmc-9999.ebuild
@@ -7,7 +7,7 @@ EAPI="2"
 ESVN_REPO_URI="https://beast-mcmc.googlecode.com/svn/trunk/"
 
 WANT_ANT_TASKS="ant-junit4"
-EANT_GENTOO_CLASSPATH="colt,jdom-1.0,itext,junit-4,jebl,matrix-toolkits-java,commons-math-2,jdom-jaxen-1.0"
+EANT_GENTOO_CLASSPATH="colt,jdom,itext,junit-4,jebl,matrix-toolkits-java,commons-math-2,jdom-jaxen-1.0"
 JAVA_ANT_REWRITE_CLASSPATH="true"
 JAVA_ANT_ENCODING="latin1"
 JAVA_PKG_BSFIX_NAME="build.xml build_BEAST_MCMC.xml build_coalsim.xml build_development.xml build_pathogen.xml build_release.xml build_treestat.xml build_vcs.xml"
@@ -26,7 +26,7 @@ IUSE=""
 
 # TODO: sys-cluster/mpijava
 COMMON_DEPS="dev-java/colt:0
-	dev-java/jdom:1.0
+	dev-java/jdom:0
 	dev-java/itext:0
 	dev-java/junit:4
 	dev-java/jebl:0
@@ -44,7 +44,7 @@ src_prepare() {
 	sed -i '/BEAST_LIB/ s|$BEAST|/usr/share/beast|' "${S}"/scripts/* || die
 	cd lib
 	rm -v colt.jar junit-*.jar itext-*.jar jdom.jar jebl.jar mtj.jar commons-math-*.jar || die
-	java-pkg_jar-from jdom-1.0
+	java-pkg_jar-from jdom
 	java-pkg_jar-from colt
 	java-pkg_jar-from itext
 	java-pkg_jar-from jebl