Fixed GitHub issue 261 - escaped line feed left in manifest when building on...

Fixed GitHub issue 261 - escaped line feed left in manifest when building on linux. Also changed name of dnaplotter jar to be consistent and because linux is case sensitive so it should exactly match the name in the script

Makefile

@@ -101,15 +101,19 @@ artemis.jar : $(CLASSES)
 	find jar_build/build -name '*.DS_Store' -print | xargs rm -rf
 	cd jar_build/build; \
 	rm -rf META-INF/MANIFEST.MF; \
-	echo "Main-Class: uk.ac.sanger.artemis.components.ArtemisMain\nPermissions: all-permissions" > manifest-art; \
+	echo "Main-Class: uk.ac.sanger.artemis.components.ArtemisMain" > manifest-art; \
+	echo "Permissions: all-permissions" >> manifest-art; \
 	jar cmf manifest-art ../artemis.jar META-INF/services images/Wellcome_Sanger_Institute_Logo_Landscape_Digital_RGB_Full_Colour.jpg images/icon.gif README.md etc \
 	                     artemis_sqlmap org uk com net htsjdk picard gov joptsimple ngs freemarker LICENSE.Apache LICENSE.Picard LICENSE.JDBC LICENSE j2ssh.properties; \
-    echo "Main-Class: uk.ac.sanger.artemis.circular.DNADraw\nPermissions: all-permissions" > manifest-circular; \
-    jar cmf manifest-circular ../DNAPlotter.jar images/Wellcome_Sanger_Institute_Logo_Landscape_Digital_RGB_Full_Colour.jpg README.md etc \
+    echo "Main-Class: uk.ac.sanger.artemis.circular.DNADraw" > manifest-circular; \
+	echo "Permissions: all-permissions" >> manifest-circular; \
+    jar cmf manifest-circular ../dnaplotter.jar images/Wellcome_Sanger_Institute_Logo_Landscape_Digital_RGB_Full_Colour.jpg README.md etc \
                          org uk com net htsjdk picard gov joptsimple ngs freemarker LICENSE.Apache LICENSE.Picard LICENSE.JDBC LICENSE j2ssh.properties; \
-	echo "Main-Class: uk.ac.sanger.artemis.components.alignment.BamView\nPermissions: all-permissions" > manifest-bamview; \
+	echo "Main-Class: uk.ac.sanger.artemis.components.alignment.BamView" > manifest-bamview; \
+	echo "Permissions: all-permissions" >> manifest-bamview; \
 	jar cmf manifest-bamview ../bamview.jar META-INF/services etc org uk com net htsjdk picard gov joptsimple ngs freemarker LICENSE.Apache LICENSE.Picard LICENSE.JDBC LICENSE; \
-	echo "Main-Class: uk.ac.sanger.artemis.components.ActMain\nPermissions: all-permissions" > manifest-act; \
+	echo "Main-Class: uk.ac.sanger.artemis.components.ActMain" > manifest-act; \
+	echo "Permissions: all-permissions" >> manifest-act; \
 	jar cmf manifest-act ../act.jar META-INF/services images/Wellcome_Sanger_Institute_Logo_Landscape_Digital_RGB_Full_Colour.jpg images/icon.gif README.md etc \
 	                     artemis_sqlmap org uk com net htsjdk picard gov joptsimple ngs freemarker LICENSE.Apache LICENSE.Picard LICENSE.JDBC LICENSE j2ssh.properties; \