diff --git a/ChangeLog b/ChangeLog
index 9c7cc1480e9254fe93e0b6a19575755acd14de09..b5f125458213eaf75979837e99416bc10d08ba7f 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,12 +1,14 @@
 Version 18
 
 	1) Switched build process to use Maven. Changed directory structure. Removed ant and Make files.
-	2) Retired a number of jars and upgraded others. Removed the ssh plugin jar as it's not used.
+	2) Retired a number of jars and upgraded others. Removed the ssh-plugin jar.
 	3) Upgraded to Picard 2.18.14 jar, which has a number of important bug fixes. 
-	4) Removed old documentation functionality. HTML/PDF manuals are now stored in gh-pages and generated from a word doc.
-	5) Changed application scripts jar paths.
+	4) Removed old documentation functionality. HTML/PDF manuals are now stored in gh-pages branch and exported directly from a word doc.
+	5) Changed application script jar paths.
 	6) Rewrote writedb_entry script.
-	7) 
+	7) Replaced script usage of -Dcom.apple.mrj.application.apple.menu.about.name with -Xdock:name.
+	8) Fixed incorrect Amigo GO term URL, used in the Artemis gene builder window.
+	9) Updated README.
 	
 Version 17.0.2-test - patch release for Sanger. Changes incorporated into GitHub master.
  
diff --git a/act b/act
index 02cd51e223fb51dbae2891baca22b3df3aa9022a..88286250168f950f002ee61f030ea1aaef8078d9 100755
--- a/act
+++ b/act
@@ -138,7 +138,7 @@ then
     echo "Starting ACT with arguments: $FLAGS $APPLICATION_PROPERTIES $*"
 fi
 
-$JAVA $FLAGS $APPLICATION_PROPERTIES -cp ".:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED" uk.ac.sanger.artemis.components.ActMain $*
+$JAVA $FLAGS $APPLICATION_PROPERTIES -cp "$APPLICATION_HOME:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED" uk.ac.sanger.artemis.components.ActMain $*
 result=$?
 
 exit $result
diff --git a/art b/art
index f3413f1e633e634a1596e1a579a9c36262b37182..85930e5a102298b54d3ccda08cac608548e8fdde 100755
--- a/art
+++ b/art
@@ -144,7 +144,7 @@ then
     echo "Starting Artemis with arguments: $FLAGS $APPLICATION_PROPERTIES $*"
 fi
 
-$JAVA $FLAGS $APPLICATION_PROPERTIES -cp ".:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED" uk.ac.sanger.artemis.components.ArtemisMain $*
+$JAVA $FLAGS $APPLICATION_PROPERTIES -cp "$APPLICATION_HOME:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED" uk.ac.sanger.artemis.components.ArtemisMain $*
 result=$?
 
 exit $result
diff --git a/bamview b/bamview
index 30b8d603d9f82bc24967cfe51b0093e0d429140e..cf64667a06b7178fc82f35af62e35eabf7aeeca5 100755
--- a/bamview
+++ b/bamview
@@ -82,7 +82,7 @@ then
     echo "Starting BamView with arguments: $FLAGS $APPLICATION_PROPERTIES $*"
 fi
 
-$JAVA $FLAGS $APPLICATION_PROPERTIES -cp ".:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED" uk.ac.sanger.artemis.components.alignment.BamView $*
+$JAVA $FLAGS $APPLICATION_PROPERTIES -cp "$APPLICATION_HOME:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED" uk.ac.sanger.artemis.components.alignment.BamView $*
 result=$?
 
 exit $result
diff --git a/dnaplotter b/dnaplotter
index a0f36b4c046da8f7f4157c0c635176b48d5960c6..fe9e835fa6507aaee6d4b1a4979054c2f66b4447 100755
--- a/dnaplotter
+++ b/dnaplotter
@@ -119,7 +119,7 @@ then
     echo "Starting DNA Plotter with arguments: $FLAGS $APPLICATION_PROPERTIES $TEMPLATE_FILE_ARG"
 fi
 
-$JAVA $FLAGS $APPLICATION_PROPERTIES -cp ".:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED" uk.ac.sanger.artemis.circular.DNADraw $TEMPLATE_FILE_ARG
+$JAVA $FLAGS $APPLICATION_PROPERTIES -cp "$APPLICATION_HOME:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED" uk.ac.sanger.artemis.circular.DNADraw $TEMPLATE_FILE_ARG
 result=$?
 
 exit $result
diff --git a/etc/writedb_entry b/etc/writedb_entry
index 1fccd24b10295fe111786570965eb2f0b9d2637b..60c9e46ccf62c14760bb86de6acbd7d3522c8f38 100755
--- a/etc/writedb_entry
+++ b/etc/writedb_entry
@@ -6,9 +6,8 @@
 # writedb_entry -help
 # writedb_entry -s Pf3D7_01 Pf3D7_05 Pf3D7_07
 #
-# The Java JRE to use is taken from the ARTEMIS_JAVA_JRE
-# environment variable. If this is not set then the JRE is defaulted to 
-# a Java 8 version.
+# If the environment variable ARTEMIS_JAVA_JRE points to a Java JRE
+# then this JRE will be used in preference to any other.
 #
 
 QUIET=no
@@ -55,7 +54,8 @@ FLAGS="-mx2048m -ms20m -Djdbc.drivers=org.postgresql.Driver -Dibatis"
 DEFAULT_CONNECTION="-Dchado=db.genedb.org:5432/snapshot?genedb_ro -Dread_only"
 APPLICATION_HOME=`dirname "$PRG"`/..
 JAR_NAME=artemis.jar
-JAR_FILE=$APPLICATION_HOME/target/unix-jars/$JAR_NAME
+JAR_FILE_DEFAULT=$APPLICATION_HOME/target/unix-jars/$JAR_NAME
+JAR_FILE_INSTALLED=$APPLICATION_HOME/$JAR_NAME
 
 #
 # Use a custom Java version if necessary
@@ -106,10 +106,9 @@ done
 if [[ "$QUIET" = "no" ]]
 then
     echo "Starting writedb_entry with arguments: $PROXY_SETTINGS $DEFAULT_CONNECTION $FLAGS $@"
-    echo "Classpath: $CLASSPATH"
 fi
 
-$JAVA $PROXY_SETTINGS $DEFAULT_CONNECTION $FLAGS -cp "$JAR_FILE" uk.ac.sanger.artemis.io.ReadAndWriteEntry "$@"
+$JAVA $PROXY_SETTINGS $DEFAULT_CONNECTION $FLAGS -cp "$APPLICATION_HOME:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED" uk.ac.sanger.artemis.io.ReadAndWriteEntry "$@"
 result=$?
 
 exit $result
diff --git a/src/assembly/unix-release-assembly.xml b/src/assembly/unix-release-assembly.xml
index 543f5a682d110de99e4c5497b98deba9b06ce137..e2a3d2b10aeb7d6d9d9a54eb365e2bf5d02ff067 100644
--- a/src/assembly/unix-release-assembly.xml
+++ b/src/assembly/unix-release-assembly.xml
@@ -21,6 +21,15 @@
 				<include>*.jar</include>
 			</includes>
 		</fileSet>
+		<fileSet>
+			<outputDirectory>${unix.assembly.folder}</outputDirectory>
+			<includes>
+				<include>etc/**</include>
+			</includes>
+			<directoryMode>0755</directoryMode>
+			<fileMode>0755</fileMode>
+			<lineEnding>unix</lineEnding>
+		</fileSet>
 		<fileSet>
 			<outputDirectory>${unix.assembly.folder}</outputDirectory>
 			<includes>