Merge branch 'improvement/JAL-3848_slivka_0.8_updated_jslib' of https://source.jalvie...

diff --git a/build.gradle b/build.gradle
index 180d4ad..172f9bc 100644 (file)
--- a/build.gradle
+++ b/build.gradle
@@ -51,6 +51,7 @@ repositories {
 }
 
 
+
 // in ext the values are cast to Object. Ensure string values are cast as String (and not GStringImpl) for later use
 def string(Object o) {
   return o == null ? "" : o.toString()
@@ -1299,13 +1300,12 @@ task linkCheck(type: JavaExec) {
   args = [ "${classesDir}/${help_dir}", "-nointernet" ]
 
   def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
-  def errFOS = outFOS
   standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
     outFOS,
-    standardOutput)
+    System.out)
   errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
     outFOS,
-    errorOutput)
+    System.err)
 
   inputs.dir("${classesDir}/${help_dir}")
   outputs.file(helpLinksCheckerOutFile)
@@ -1336,6 +1336,9 @@ jar {
     "Codebase": application_codebase
   }
 
+  duplicatesStrategy "EXCLUDE"
+
+
   destinationDir = file("${jalviewDir}/${package_dir}")
   archiveName = rootProject.name+".jar"
 
@@ -1397,6 +1400,9 @@ shadowJar {
   manifest {
     attributes 'Implementation-Version': JALVIEW_VERSION
   }
+
+  duplicatesStrategy "EXCLUDE"
+
   mainClassName = shadow_jar_main_class
   mergeServiceFiles()
   classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
@@ -2418,12 +2424,12 @@ DEBUG: ${eclipseDebug}
         new org.apache.tools.ant.util.TeeOutputStream(
           logOutFOS,
           stdout),
-        standardOutput)
+        System.out)
       errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
         new org.apache.tools.ant.util.TeeOutputStream(
           logErrFOS,
           stderr),
-        errorOutput)
+        System.err)
     } else {
       standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
         logOutFOS,