Merge branch 'master' of ssh://github.com/tcarver/Artemis

Makefile

@@ -291,15 +291,15 @@ artemis.jar : $(CLASSES)
 	find jar_build -name '.svn' -print | xargs rm -rf
 	cd jar_build; \
 	rm -rf META-INF/MANIFEST.MF; \
-	echo "Main-Class: uk.ac.sanger.artemis.components.ArtemisMain" > manifest-art; \
+	echo "Main-Class: uk.ac.sanger.artemis.components.ArtemisMain\nPermissions: all-permissions" > manifest-art; \
 	jar cmf manifest-art artemis.jar META-INF/services images/PSUlogo.gif images/icon.gif README etc \
 	                     artemis_sqlmap org uk com net nsdb type seqdb LICENSE.Apache j2ssh.properties; \
-        echo "Main-Class: uk.ac.sanger.artemis.circular.DNADraw" > manifest-circular; \
+        echo "Main-Class: uk.ac.sanger.artemis.circular.DNADraw\nPermissions: all-permissions" > manifest-circular; \
         jar cmf manifest-circular DNAPlotter.jar images/PSUlogo.gif README etc \
                              uk org/gmod org/w3c org/apache org/biojava/bio/ com/ibatis/common/jdbc/ net/sf/samtools/ LICENSE.Apache j2ssh.properties; \
-	echo "Main-Class: uk.ac.sanger.artemis.components.alignment.BamView" > manifest-bamview; \
+	echo "Main-Class: uk.ac.sanger.artemis.components.alignment.BamView\nPermissions: all-permissions" > manifest-bamview; \
 	jar cmf manifest-bamview BamView.jar META-INF/services etc uk org/apache org/biojava org/biojavax org/gmod org/w3c net/sf com/ibatis; \
-	echo "Main-Class: uk.ac.sanger.artemis.components.ActMain" > manifest-act; \
+	echo "Main-Class: uk.ac.sanger.artemis.components.ActMain\nPermissions: all-permissions" > manifest-act; \
 	jar cmf manifest-act act.jar META-INF/services images/PSUlogo.gif images/icon.gif README etc \
 	                     artemis_sqlmap org uk com net nsdb type seqdb LICENSE.Apache j2ssh.properties; \
 	rm -f etc/log4j.properties; \