updated build to package JRE-11 with STEM patch from Harsha Krishnareddy
diff --git a/.gitignore b/.gitignore
index 5106459..3a69572 100644
--- a/.gitignore
+++ b/.gitignore
@@ -4,3 +4,4 @@
 .DS_Store
 .Spotlight-V100
 .Trashes
+*.class
diff --git a/org.eclipse.stem/releng/org.eclipse.stem.releng.targetplatforms/STEM4.target b/org.eclipse.stem/releng/org.eclipse.stem.releng.targetplatforms/STEM4.target
index 4478977..9858538 100644
--- a/org.eclipse.stem/releng/org.eclipse.stem.releng.targetplatforms/STEM4.target
+++ b/org.eclipse.stem/releng/org.eclipse.stem.releng.targetplatforms/STEM4.target
@@ -28,9 +28,10 @@
 			<unit id="org.eclipse.help.ui" version="4.2.100.v20200923-2139"/>
 			<repository location="http://download.eclipse.org/eclipse/updates/4.18"/>
 		</location>
-		<location includeAllPlatforms="false" includeConfigurePhase="true" includeMode="planner" includeSource="true" type="InstallableUnit">
-    		<repository location="https://download.eclipse.org/justj/jres/11/updates/release/11.0.2"/>
-    		<unit id="org.eclipse.justj.openjdk.hotspot.jre.full" version="0.0.0"/>
+		<location>
+			<unit id="org.eclipse.justj.openjdk.hotspot.jre.full" version="11.0.2.v20200815-0835"/>
+			<unit id="a.jre.org.eclipse.justj.openjdk.hotspot.jre.full" version="11.0.0"/>
+			<repository location="https://download.eclipse.org/justj/jres/11/updates/release/latest/"/>
 		</location>
 	</locations>
 </target>
\ No newline at end of file
diff --git a/org.eclipse.stem/releng/org.eclipse.stem.tycho.configuration/pom.xml b/org.eclipse.stem/releng/org.eclipse.stem.tycho.configuration/pom.xml
index 86cfbc7..36d4c4e 100755
--- a/org.eclipse.stem/releng/org.eclipse.stem.tycho.configuration/pom.xml
+++ b/org.eclipse.stem/releng/org.eclipse.stem.tycho.configuration/pom.xml
@@ -32,19 +32,17 @@
 			<layout>p2</layout>
 		</repository>
 		<repository>
-      		<id>justj</id>
-      		<url>https://download.eclipse.org/justj/jres/11/updates/release/latest/</url>
-      		<layout>p2</layout>
- 		</repository>
+			<id>justj</id>
+			<url>https://download.eclipse.org/justj/jres/11/updates/release/latest/</url>
+			<layout>p2</layout>
+		</repository>
 	</repositories>
-	
 	<pluginRepositories>
 		<pluginRepository>
 			<id>tycho-snapshots</id>
 			<url>https://repo.eclipse.org/content/repositories/tycho-snapshots/</url>
 		</pluginRepository>
 	</pluginRepositories>
-	
 	<build>
 		<!-- To use the plugin goals in your POM or parent POM -->
 		<plugins>
@@ -53,7 +51,6 @@
 				<artifactId>tycho-p2-repository-plugin</artifactId>
 				<version>2.2.0</version>
 			</plugin>
-			
 			<plugin>
 				<groupId>org.eclipse.tycho</groupId>
 				<artifactId>tycho-maven-plugin</artifactId>
@@ -83,31 +80,12 @@
 				<version>${tycho.version}</version>
 				<configuration>
 					<environments>
-						<!-- 
-						<environment>
-							<os>linux</os>
-							<ws>gtk</ws>
-							<arch>x86</arch>
-						</environment>
-						-->
 						<environment>
 							<os>linux</os>
 							<ws>gtk</ws>
 							<arch>x86_64</arch>
 						</environment>
 						<environment>
-							<os>linux</os>
-							<ws>gtk</ws>
-							<arch>ppc64le</arch>
-						</environment>
-						<!--   
-						<environment>
-							<os>win32</os>.
-							<ws>win32</ws>
-							<arch>x86</arch> 
-						</environment>
-						-->
-						<environment>
 							<os>win32</os>
 							<ws>win32</ws>
 							<arch>x86_64</arch>
@@ -118,10 +96,15 @@
 							<arch>x86_64</arch>
 						</environment>
 					</environments>
-					<!--workaround bug 532302: set EE to JavASE-11 to make sure we resolve 
-						Import-Package: javax.annoation against bundle javax.annotation (as opposed 
-						to system package from bundle's BREE JavaSE-1.8) -->
+					<!--  for dev enironment -->
 					<executionEnvironment>JavaSE-11</executionEnvironment>
+					<!--  for distribution build -->
+					<executionEnvironmentDefault>org.eclipse.justj.openjdk.hotspot.jre.full-11</executionEnvironmentDefault>
+					<dependency-resolution>
+						<profileProperties>
+							<org.eclipse.justj.buildtime>true</org.eclipse.justj.buildtime>
+						</profileProperties>
+					</dependency-resolution>
 				</configuration>
 			</plugin>
 		</plugins>
diff --git a/org.eclipse.stem/releng/org.eclipse.stem.tycho.product/STEM.product b/org.eclipse.stem/releng/org.eclipse.stem.tycho.product/STEM.product
index c3cdb3c..4d437ef 100644
--- a/org.eclipse.stem/releng/org.eclipse.stem.tycho.product/STEM.product
+++ b/org.eclipse.stem/releng/org.eclipse.stem.tycho.product/STEM.product
@@ -1,25 +1,19 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <?pde version="3.5"?>
-
 <product name="STEM" uid="org.eclipse.stem.tycho.product" id="org.eclipse.stem.ui.product" application="org.eclipse.stem.ui.CoreEditorAdvisorApplication" version="4.0.0.qualifier" useFeatures="true" includeLaunchers="true">
-
    <aboutInfo>
       <image path="/org.eclipse.stem.ui/branding/ohf64_64_32.gif"/>
       <text>
          STEM - Spatiotemporal Epidemological Modeler
       </text>
    </aboutInfo>
-
    <configIni use="default">
    </configIni>
-
    <launcherArgs>
       <vmArgsMac>-XstartOnFirstThread -Dorg.eclipse.swt.internal.carbon.smallFonts
       </vmArgsMac>
    </launcherArgs>
-
    <windowImages i16="/org.eclipse.stem.tycho.product/branding/STEM4_16.bmp" i32="/org.eclipse.stem.tycho.product/branding/STEM4_32.bmp" i48="/org.eclipse.stem.tycho.product/branding/STEM4_48.bmp" i64="/org.eclipse.stem.tycho.product/branding/STEM4_64.bmp" i128="/org.eclipse.stem.tycho.product/branding/STEM4_128.bmp" i256="/org.eclipse.stem.tycho.product/branding/STEM4_256.bmp"/>
-
    <splash
       location="org.eclipse.stem.ui" />
    <launcher name="STEM">
@@ -36,14 +30,11 @@
             winExtraLargeHigh="branding/STEM4_256.bmp"/>
       </win>
    </launcher>
-
-
    <vm>
       <linux include="true">org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-11</linux>
       <macos include="true">org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-11</macos>
       <windows include="true">org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-11</windows>
    </vm>
-
    <license>
         <url>http://eclipse.org/legal/epl/notice.php</url>
         <text>
@@ -173,420 +164,28 @@
 155
          </text>
    </license>
-
    <plugins>
-      <plugin id="com.google.guava"/>
-      <plugin id="com.google.inject"/>
-      <plugin id="com.ibm.icu"/>
-      <plugin id="com.jcraft.jsch"/>
-      <plugin id="com.sun.el"/>
-      <plugin id="javax.annotation"/>
-      <plugin id="javax.el"/>
-      <plugin id="javax.inject"/>
-      <plugin id="javax.servlet"/>
-      <plugin id="javax.servlet.jsp"/>
-      <plugin id="org.antlr.runtime"/>
-      <plugin id="org.apache.ant"/>
-      <plugin id="org.apache.batik.css"/>
-      <plugin id="org.apache.batik.dom"/>
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-      <plugin id="org.apache.batik.util"/>
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-      <plugin id="org.apache.commons.jxpath"/>
-      <plugin id="org.apache.commons.lang"/>
-      <plugin id="org.apache.commons.logging"/>
-      <plugin id="org.apache.commons.math3"/>
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-      <plugin id="org.apache.felix.gogo.shell"/>
-      <plugin id="org.apache.felix.scr"/>
-      <plugin id="org.apache.jasper.glassfish"/>
-      <plugin id="org.apache.log4j"/>
-      <plugin id="org.apache.lucene.analyzers-common"/>
-      <plugin id="org.apache.lucene.analyzers-smartcn"/>
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-      <plugin id="org.eclipse.stem.ui.diseasemodels.externaldatasource"/>
-      <plugin id="org.eclipse.stem.ui.diseasemodels.forcing"/>
-      <plugin id="org.eclipse.stem.ui.diseasemodels.globalinfluenzamodel"/>
-      <plugin id="org.eclipse.stem.ui.diseasemodels.multipopulation"/>
-      <plugin id="org.eclipse.stem.ui.diseasemodels.vector"/>
-      <plugin id="org.eclipse.stem.ui.foodproduction"/>
-      <plugin id="org.eclipse.stem.ui.ge"/>
-      <plugin id="org.eclipse.stem.ui.grapheditor"/>
-      <plugin id="org.eclipse.stem.ui.graphgenerators"/>
-      <plugin id="org.eclipse.stem.ui.headless"/>
-      <plugin id="org.eclipse.stem.ui.interventions"/>
-      <plugin id="org.eclipse.stem.ui.loggers"/>
-      <plugin id="org.eclipse.stem.ui.populationmodels"/>
-      <plugin id="org.eclipse.stem.ui.reports"/>
-      <plugin id="org.eclipse.stem.ui.solvers.fd"/>
-      <plugin id="org.eclipse.stem.ui.solvers.rk"/>
-      <plugin id="org.eclipse.stem.ui.solvers.stochastic"/>
-      <plugin id="org.eclipse.stem.ui.transport"/>
-      <plugin id="org.eclipse.stem.util.analysis"/>
-      <plugin id="org.eclipse.stem.util.loggers"/>
-      <plugin id="org.eclipse.swt"/>
-      <plugin id="org.eclipse.swt.cocoa.macosx.x86_64" fragment="true"/>
-      <plugin id="org.eclipse.team.core"/>
-      <plugin id="org.eclipse.team.genericeditor.diff.extension"/>
-      <plugin id="org.eclipse.team.ui"/>
-      <plugin id="org.eclipse.text"/>
-      <plugin id="org.eclipse.tools.layout.spy"/>
-      <plugin id="org.eclipse.ui"/>
-      <plugin id="org.eclipse.ui.browser"/>
-      <plugin id="org.eclipse.ui.cheatsheets"/>
-      <plugin id="org.eclipse.ui.cocoa" fragment="true"/>
-      <plugin id="org.eclipse.ui.console"/>
-      <plugin id="org.eclipse.ui.editors"/>
-      <plugin id="org.eclipse.ui.externaltools"/>
-      <plugin id="org.eclipse.ui.forms"/>
-      <plugin id="org.eclipse.ui.genericeditor"/>
-      <plugin id="org.eclipse.ui.ide"/>
-      <plugin id="org.eclipse.ui.ide.application"/>
-      <plugin id="org.eclipse.ui.intro"/>
-      <plugin id="org.eclipse.ui.intro.quicklinks"/>
-      <plugin id="org.eclipse.ui.intro.universal"/>
-      <plugin id="org.eclipse.ui.monitoring"/>
-      <plugin id="org.eclipse.ui.navigator"/>
-      <plugin id="org.eclipse.ui.navigator.resources"/>
-      <plugin id="org.eclipse.ui.net"/>
-      <plugin id="org.eclipse.ui.themes"/>
-      <plugin id="org.eclipse.ui.trace"/>
-      <plugin id="org.eclipse.ui.views"/>
-      <plugin id="org.eclipse.ui.views.log"/>
-      <plugin id="org.eclipse.ui.views.properties.tabbed"/>
-      <plugin id="org.eclipse.ui.workbench"/>
-      <plugin id="org.eclipse.ui.workbench.texteditor"/>
-      <plugin id="org.eclipse.update.configurator"/>
-      <plugin id="org.eclipse.xtend.core"/>
-      <plugin id="org.eclipse.xtend.lib"/>
-      <plugin id="org.eclipse.xtend.lib.macro"/>
-      <plugin id="org.eclipse.xtext"/>
-      <plugin id="org.eclipse.xtext.builder"/>
-      <plugin id="org.eclipse.xtext.common.types"/>
-      <plugin id="org.eclipse.xtext.common.types.edit"/>
-      <plugin id="org.eclipse.xtext.common.types.shared"/>
-      <plugin id="org.eclipse.xtext.common.types.shared.jdt38" fragment="true"/>
-      <plugin id="org.eclipse.xtext.common.types.ui"/>
-      <plugin id="org.eclipse.xtext.ecore"/>
-      <plugin id="org.eclipse.xtext.logging" fragment="true"/>
-      <plugin id="org.eclipse.xtext.smap"/>
-      <plugin id="org.eclipse.xtext.ui"/>
-      <plugin id="org.eclipse.xtext.ui.codetemplates"/>
-      <plugin id="org.eclipse.xtext.ui.codetemplates.ui"/>
-      <plugin id="org.eclipse.xtext.ui.ecore"/>
-      <plugin id="org.eclipse.xtext.ui.shared"/>
-      <plugin id="org.eclipse.xtext.util"/>
-      <plugin id="org.eclipse.xtext.xbase"/>
-      <plugin id="org.eclipse.xtext.xbase.lib"/>
-      <plugin id="org.eclipse.xtext.xbase.ui"/>
-      <plugin id="org.eclipse.zest.core"/>
-      <plugin id="org.eclipse.zest.layouts"/>
-      <plugin id="org.hamcrest.core"/>
-      <plugin id="org.junit"/>
-      <plugin id="org.junit.jupiter.api"/>
-      <plugin id="org.junit.jupiter.engine"/>
-      <plugin id="org.junit.jupiter.migrationsupport"/>
-      <plugin id="org.junit.jupiter.params"/>
-      <plugin id="org.junit.platform.commons"/>
-      <plugin id="org.junit.platform.engine"/>
-      <plugin id="org.junit.platform.launcher"/>
-      <plugin id="org.junit.platform.runner"/>
-      <plugin id="org.junit.platform.suite.api"/>
-      <plugin id="org.junit.vintage.engine"/>
-      <plugin id="org.mozilla.javascript"/>
-      <plugin id="org.objectweb.asm"/>
-      <plugin id="org.objectweb.asm.tree"/>
-      <plugin id="org.opentest4j"/>
-      <plugin id="org.sat4j.core"/>
-      <plugin id="org.sat4j.pb"/>
-      <plugin id="org.tukaani.xz"/>
-      <plugin id="org.w3c.css.sac"/>
-      <plugin id="org.w3c.dom.events"/>
-      <plugin id="org.w3c.dom.smil"/>
-      <plugin id="org.w3c.dom.svg"/>
+      <plugin id="org.eclipse.justj.openjdk.hotspot.jre.full"/>
    </plugins>
-
    <features>
       <feature id="org.eclipse.stem.product.feature" version="3.0.0.qualifier"/>
       <feature id="org.eclipse.stem.modelgen" version="3.0.0.qualifier"/>
-      <!--
       <feature id="org.eclipse.justj.openjdk.hotspot.jre.full" installMode="root"/>
-      -->
    </features>
-
    <configurations>
       <plugin id="org.apache.felix.scr" autoStart="true" startLevel="2" />
       <plugin id="org.eclipse.core.runtime" autoStart="true" startLevel="0" />
       <plugin id="org.eclipse.equinox.common" autoStart="true" startLevel="2" />
       <plugin id="org.eclipse.equinox.event" autoStart="true" startLevel="2" />
       <plugin id="org.eclipse.equinox.simpleconfigurator" autoStart="true" startLevel="1" />
-      <property name="stem.buildId" value="4.0.0_v" />
+      <property name="stem.buildId" value="4.0.3_20210303184801" />
    </configurations>
-
    <repositories>
       <repository location="http://download.eclipse.org/stem/update-site/" enabled="true" />
    </repositories>
-
    <preferencesInfo>
       <targetfile overwrite="false"/>
    </preferencesInfo>
-
    <cssInfo>
    </cssInfo>
-
-</product>
+</product>
\ No newline at end of file
diff --git a/workspace/.metadata/.log b/workspace/.metadata/.log
index 1a64556..138858f 100644
--- a/workspace/.metadata/.log
+++ b/workspace/.metadata/.log
@@ -1365,3 +1365,60 @@
 !MESSAGE Unexpected error loading extension: org.eclipse.equinox.p2.artifact.repository.XZedRepository
 !STACK 0
 java.lang.NullPointerException
+!SESSION 2021-03-03 17:40:06.950 -----------------------------------------------
+eclipse.buildId=unknown
+java.version=11.0.8
+java.vendor=Oracle Corporation
+BootLoader constants: OS=macosx, ARCH=x86_64, WS=cocoa, NL=en_US
+Framework arguments:  -eclipse.keyring /var/folders/9l/5blrkn7958s7zckzxhlmxj540000gq/T/tycho12982477274668588306secure_storage
+Command-line arguments:  -eclipse.keyring /var/folders/9l/5blrkn7958s7zckzxhlmxj540000gq/T/tycho12982477274668588306secure_storage
+
+!ENTRY org.eclipse.equinox.p2.transport.ecf 2 0 2021-03-03 17:40:06.950
+!MESSAGE Connection to https://ftp.halifax.rwth-aachen.de/eclipse/releases/2021-03/202102261000/plugins/org.eclipse.ecf.provider.filetransfer_3.2.601.v20201025-0700.jar.pack.gz failed on Connect to ftp.halifax.rwth-aachen.de:443 [ftp.halifax.rwth-aachen.de/2a00:8a60:e012:a00:0:0:0:21] failed: No route to host (connect failed). Retry attempt 0 started
+!STACK 0
+org.apache.http.conn.HttpHostConnectException: Connect to ftp.halifax.rwth-aachen.de:443 [ftp.halifax.rwth-aachen.de/2a00:8a60:e012:a00:0:0:0:21] failed: No route to host (connect failed)
+	at org.apache.http.impl.conn.DefaultHttpClientConnectionOperator.connect(DefaultHttpClientConnectionOperator.java:156)
+	at org.apache.http.impl.conn.PoolingHttpClientConnectionManager.connect(PoolingHttpClientConnectionManager.java:374)
+	at org.apache.http.impl.execchain.MainClientExec.establishRoute(MainClientExec.java:393)
+	at org.apache.http.impl.execchain.MainClientExec.execute(MainClientExec.java:236)
+	at org.apache.http.impl.execchain.ProtocolExec.execute(ProtocolExec.java:186)
+	at org.apache.http.impl.execchain.RetryExec.execute(RetryExec.java:89)
+	at org.apache.http.impl.execchain.RedirectExec.execute(RedirectExec.java:110)
+	at org.apache.http.impl.client.InternalHttpClient.doExecute(InternalHttpClient.java:185)
+	at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:83)
+	at org.eclipse.ecf.provider.filetransfer.httpclient45.HttpClientRetrieveFileTransfer.performConnect(HttpClientRetrieveFileTransfer.java:1003)
+	at org.eclipse.ecf.provider.filetransfer.httpclient45.HttpClientRetrieveFileTransfer.access$0(HttpClientRetrieveFileTransfer.java:995)
+	at org.eclipse.ecf.provider.filetransfer.httpclient45.HttpClientRetrieveFileTransfer$1.performFileTransfer(HttpClientRetrieveFileTransfer.java:991)
+	at org.eclipse.ecf.filetransfer.FileTransferJob.run(FileTransferJob.java:76)
+	at org.eclipse.core.internal.jobs.Worker.run(Worker.java:63)
+Caused by: java.net.ConnectException: No route to host (connect failed)
+	at java.base/java.net.PlainSocketImpl.socketConnect(Native Method)
+	at java.base/java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:399)
+	at java.base/java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:242)
+	at java.base/java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:224)
+	at java.base/java.net.SocksSocketImpl.connect(SocksSocketImpl.java:403)
+	at java.base/java.net.Socket.connect(Socket.java:608)
+	at org.apache.http.conn.ssl.SSLConnectionSocketFactory.connectSocket(SSLConnectionSocketFactory.java:368)
+	at org.apache.http.impl.conn.DefaultHttpClientConnectionOperator.connect(DefaultHttpClientConnectionOperator.java:142)
+	... 13 more
+
+!ENTRY org.eclipse.equinox.p2.director 0 0 2021-03-03 17:45:41.150
+!MESSAGE Overall install request is satisfiable
+!SUBENTRY 1 org.eclipse.equinox.p2.director 0 0 2021-03-03 17:45:41.150
+!MESSAGE Add request for STEM 4.0.0.202103040136 (org.eclipse.stem.tycho.product 4.0.0.202103040136) is satisfiable
+!SUBENTRY 1 org.eclipse.equinox.p2.director 0 0 2021-03-03 17:45:41.150
+!MESSAGE Add request for JustJ OpenJDK Hotspot JRE Complete 11.0.2.v20200815-0835 (org.eclipse.justj.openjdk.hotspot.jre.full.feature.group 11.0.2.v20200815-0835) is satisfiable
+
+!ENTRY org.eclipse.equinox.p2.director 0 0 2021-03-03 17:45:53.247
+!MESSAGE Overall install request is satisfiable
+!SUBENTRY 1 org.eclipse.equinox.p2.director 0 0 2021-03-03 17:45:53.247
+!MESSAGE Add request for STEM 4.0.0.202103040136 (org.eclipse.stem.tycho.product 4.0.0.202103040136) is satisfiable
+!SUBENTRY 1 org.eclipse.equinox.p2.director 0 0 2021-03-03 17:45:53.247
+!MESSAGE Add request for JustJ OpenJDK Hotspot JRE Complete 11.0.2.v20200815-0835 (org.eclipse.justj.openjdk.hotspot.jre.full.feature.group 11.0.2.v20200815-0835) is satisfiable
+
+!ENTRY org.eclipse.equinox.p2.director 0 0 2021-03-03 17:46:03.307
+!MESSAGE Overall install request is satisfiable
+!SUBENTRY 1 org.eclipse.equinox.p2.director 0 0 2021-03-03 17:46:03.308
+!MESSAGE Add request for STEM 4.0.0.202103040136 (org.eclipse.stem.tycho.product 4.0.0.202103040136) is satisfiable
+!SUBENTRY 1 org.eclipse.equinox.p2.director 0 0 2021-03-03 17:46:03.308
+!MESSAGE Add request for JustJ OpenJDK Hotspot JRE Complete 11.0.2.v20200815-0835 (org.eclipse.justj.openjdk.hotspot.jre.full.feature.group 11.0.2.v20200815-0835) is satisfiable