Merge branch 'task/JAL-3337-rm-lib-update-sourceDist' into develop

diff --combined build.gradle
index 492d7c1,7746b25..0bb89f9
--- 1/build.gradle
--- 2/build.gradle
+++ b/build.gradle
@@@ -1170,67 -1170,65 +1170,71 @@@ clean 
  task sourceDist (type: Tar) {
    
    def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
 -  archiveFileName = project.name + "_" + VERSION_UNDERSCORES + ".tar.gz"
 +  def outputFileName = project.name + "_" + VERSION_UNDERSCORES + ".tar.gz"
 +  // cater for buildship < 3.1 [3.0.1 is max version in eclipse 2018-09]
 +  try {
 +    archiveFileName = outputFileName
 +  } catch (Exception e) {
 +    archiveName = outputFileName
 +  }
    
    compression Compression.GZIP
    
-   from jalviewDir
    into project.name
-  
-    
-   exclude (".*")
-   exclude ("**/.*")
-   exclude ("*.class")
-   exclude ("**/*.class")
-   include (eclipse_extra_jdt_prefs_file)
-   include ("AUTHORS")
-   include ("CITATION")
-   include ("FEATURETODO")
-   include ("JAVA-11-README")
-   include ("FEATURETODO")
-   include ("LICENSE")
-   include ("README")
-   include ("RELEASE")
-   include ("THIRDPARTYLIBS")
-   include ("build.gradle")
-   include ("gradle.properties")
-   include ("$sourceDir/*.java")
-   include ("$sourceDir/**/*.java")
-   include ("$sourceDir/**/*.cdr")
-   include ("$j8libDir/**/*.jar")
-   include ("$j11libDir/**/*.jar")
-   include ("$resourceDir/**/*")
-   include ("$helpDir/**/*")
-   include ("$schemaDir/**/*")
-   include ("$utilsDir/**/*")
-   include ("$docDir/**/*")
-   include ("$examplesDir/**/*")
-   include ("getdown/**/*")
-   //include ("jalview-jalopy.xml")
-   //include ("JalviewApplet.jpx")
-   //include ("JalviewX.jpx")
-   //include ("nbbuild.xml")
-   //include ("nbproject/genfiles.properties")
-   //include ("nbproject/project.properties")
-   //include ("nbproject/project.xml")
-   
+ 
+   def EXCLUDE_FILES=["build/*","bin/*","test-output/","test-reports","tests","clover*/*"
+   ,".*"
+   ,"benchmarking/*"
+   ,"**/.*"
+   ,"*.class"
+   ,"**/*.class","$j11modDir/**/*.jar","appletlib","**/*locales"
+   ,"*locales/**",
+   ,"utils/InstallAnywhere"] 
+   def PROCESS_FILES=[   "AUTHORS",
+   "CITATION",
+   "FEATURETODO",
+   "JAVA-11-README",
+   "FEATURETODO",
+   "LICENSE",
+   "**/README",
+   "RELEASE",
+   "THIRDPARTYLIBS","TESTNG",
+   "build.gradle",
+   "gradle.properties",
+   "**/*.java",
+   "**/*.html",
+   "**/*.xml",
+   "**/*.gradle",
+   "**/*.groovy",
+   "**/*.properties",
+   "**/*.perl",
+   "**/*.sh"]
+ 
+   from(jalviewDir) {
+     exclude (EXCLUDE_FILES)
+     include (PROCESS_FILES)
+     filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['Version-Rel': JALVIEW_VERSION,'Year-Rel': getDate("yyyy")])
+   }
+   from(jalviewDir) {
+     exclude (EXCLUDE_FILES)
+     exclude (PROCESS_FILES)
    exclude ("appletlib")
    exclude ("**/*locales")
    exclude ("*locales/**")
    exclude ("utils/InstallAnywhere")
-   exclude (libDir)
-   exclude (getdown_files_dir)
+ 
+     exclude (getdown_files_dir)
    exclude (getdown_website_dir)
  
    // exluding these as not using jars as modules yet
    exclude ("$j11modDir/**/*.jar")
- 
+ }
+ //  from (jalviewDir) {
+ //    // explicit includes for stuff that seemed to not get included
+ //    include(fileTree("test/**/*."))
+ //    exclude(EXCLUDE_FILES)
+ //    exclude(PROCESS_FILES)
+ //  }
  }
  
  task helppages  {