JAL-3449 merge from develop

diff --cc build.gradle
index 05fddc0,ba884a1..bd31eaa
--- 1/build.gradle
--- 2/build.gradle
+++ b/build.gradle
@@@ -9,7 -8,8 +9,7 @@@ import groovy.xml.XmlUti
  
  buildscript {
    dependencies {
-     classpath 'org.openclover:clover:4.3.1'
+     classpath 'org.openclover:clover:4.4.1'
 -    classpath 'org.apache.commons:commons-compress:1.18'
    }
  }
  
@@@ -534,21 -444,15 +534,21 @@@ eclipse 
          }
        }
      }
 -  }
  
 -  //synchronizationTasks eclipseClasspath
 -  //autoBuildTasks eclipseClasspath
 +  } // jdt
 +
 +  if (IN_ECLIPSE) {
 +    // Don't want these to be activated if in headless build
 +    synchronizationTasks "eclipseSynchronizationTask"
 +    autoBuildTasks "eclipseAutoBuildTask"
 +
 +  }
  }
  
 +
  task cloverInstr() {
    // only instrument source, we build test classes as normal
-   inputs.files files (sourceSets.main.allJava) // , fileTree(dir: testSourceDir, include: ["**/*.java"]))
+   inputs.files files (sourceSets.main.allJava,sourceSets.test.allJava) // , fileTree(dir:"$jalviewDir/$testSourceDir", include: ["**/*.java"]))
    outputs.dir cloverInstrDir
  
    doFirst {