Index: build.gradle
===================================================================
diff -u -N -rcc9e776268c8713dc69ee6efc09a5f9f4d4ae9cd -r295ae63db251a5b3006c39e4364dd8576e4f4427
--- build.gradle	(.../build.gradle)	(revision cc9e776268c8713dc69ee6efc09a5f9f4d4ae9cd)
+++ build.gradle	(.../build.gradle)	(revision 295ae63db251a5b3006c39e4364dd8576e4f4427)
@@ -1363,8 +1363,16 @@
   }
 }
 
-task jalviewjsEclipseCopyDropins {
+task eclipseSetup {
+  dependsOn eclipseProject
+  dependsOn eclipseClasspath
+  dependsOn eclipseJdt
+}
+
+/* using the Copy task below
+task OLDjalviewjsEclipseCopyDropins {
   dependsOn jalviewjsEclipsePaths
+  dependsOn jalviewjsCleanEclipse
   def inputFiles = fileTree(dir: utilsDropinsDir, include: "*.jar")
   def outputDir = eclipseDropinsDir
 
@@ -1382,14 +1390,43 @@
     }
   }
 }
+*/
 
 // this version (type: Copy) will delete anything in the eclipse dropins folder that isn't in fromDropinsDir
-task NEWjalviewjsEclipseCopyDropins(type: Copy) {
+task jalviewjsEclipseCopyDropins(type: Copy) {
   dependsOn jalviewjsEclipsePaths
+
   from utilsDropinsDir
   into eclipseDropinsDir
 }
 
+// this eclipse -clean doesn't actually work
+task jalviewjsCleanEclipse(type: Exec) {
+  dependsOn eclipseSetup
+  dependsOn jalviewjsEclipsePaths
+  dependsOn jalviewjsEclipseCopyDropins
+
+  executable(eclipseBinary)
+  args(["-nosplash", "--launcher.suppressErrors", "-data", eclipseWorkspace.getPath(), "-clean", "-console", "-consoleLog"])
+  if (eclipseDebug) {
+    args += "-debug"
+  }
+  args += "-l"
+
+  def inputString = """exit
+y
+"""
+  def inputByteStream = new ByteArrayInputStream(inputString.getBytes())
+  standardInput = inputByteStream
+
+  doFirst {
+    println("CLEAN ECLIPSE_DEBUG=${eclipseDebug}")
+  }
+}
+/* not really working yet
+jalviewjsEclipseCopyDropins.finalizedBy jalviewjsCleanEclipse
+*/
+
 task jalviewjsUnzipFiles {
   dependsOn jalviewjsSitePath
 
@@ -1472,9 +1509,7 @@
 }
 
 task jalviewjsProjectImport(type: Exec) {
-  dependsOn eclipseProject
-  dependsOn eclipseClasspath
-  dependsOn eclipseJdt
+  dependsOn eclipseSetup
   dependsOn jalviewjsEclipsePaths
   dependsOn jalviewjsEclipseSetup
 
Index: gradle.properties
===================================================================
diff -u -N -r2bac51d2121543d6784db7c4c5f9cea595c02778 -r295ae63db251a5b3006c39e4364dd8576e4f4427
--- gradle.properties	(.../gradle.properties)	(revision 2bac51d2121543d6784db7c4c5f9cea595c02778)
+++ gradle.properties	(.../gradle.properties)	(revision 295ae63db251a5b3006c39e4364dd8576e4f4427)
@@ -146,9 +146,9 @@
 eclipse_extra_jdt_prefs_file = .settings/org.eclipse.jdt.core.jalview.prefs
 eclipse_project_name = jalview
 eclipse_bin_dir = bin
-eclipse_debug = true
+eclipse_debug = false
 
-jalviewjs_eclipse_root = ~/buildtools/eclipse/jee-2019-06
+jalviewjs_eclipse_root = ~/buildtools/eclipse/jee-2019-09
 
 jalviewjs_utils_dir = utils/jalviewjs
 jalviewjs_eclipse_dropins_dir = eclipse/dropins
Index: utils/jalviewjs/SwingJS-site.zip_4.12
===================================================================
diff -u -N -r2bac51d2121543d6784db7c4c5f9cea595c02778 -r295ae63db251a5b3006c39e4364dd8576e4f4427
Binary files differ
Index: utils/jalviewjs/SwingJS-site.zip_4.13
===================================================================
diff -u -N -r2bac51d2121543d6784db7c4c5f9cea595c02778 -r295ae63db251a5b3006c39e4364dd8576e4f4427
Binary files differ
Index: utils/jalviewjs/eclipse/cleanEclipseOptions
===================================================================
diff -u -N
--- utils/jalviewjs/eclipse/cleanEclipseOptions	(revision 0)
+++ utils/jalviewjs/eclipse/cleanEclipseOptions	(revision 295ae63db251a5b3006c39e4364dd8576e4f4427)
@@ -0,0 +1,3 @@
+org.eclipse.equinox.p2.core/debug=true
+org.eclipse.equinox.p2.core/reconciler=true
+
Index: utils/jalviewjs/eclipse/dropins/com.seeq.eclipse.importprojects.jar
===================================================================
diff -u -N
Binary files differ
Index: utils/jalviewjs/eclipse/dropins_4.12/com.seeq.eclipse.importprojects-1.4.0.jar
===================================================================
diff -u -N -ra2471f9a2d164c04e9863702195924b4d95d41c8 -r295ae63db251a5b3006c39e4364dd8576e4f4427
Binary files differ
Index: utils/jalviewjs/eclipse/dropins_4.12/net.sf.j2s.core-3.2.4-FOR_4.12.jar
===================================================================
diff -u -N -r09e8aaa14d0c425073f1b8797fb80c978b6502cf -r295ae63db251a5b3006c39e4364dd8576e4f4427
Binary files differ
Index: utils/jalviewjs/eclipse/dropins_4.13/com.seeq.eclipse.importprojects-1.4.0.jar
===================================================================
diff -u -N -ra2471f9a2d164c04e9863702195924b4d95d41c8 -r295ae63db251a5b3006c39e4364dd8576e4f4427
Binary files differ
Index: utils/jalviewjs/eclipse/dropins_4.13/net.sf.j2s.core-3.2.4.08.jar
===================================================================
diff -u -N -r438e8852c14561ff835970852159116020e08759 -r295ae63db251a5b3006c39e4364dd8576e4f4427
Binary files differ
Index: utils/jalviewjs/eclipse/unused_dropins/net.sf.j2s.core-3.2.4-FOR_4.12.jar
===================================================================
diff -u -N -r438e8852c14561ff835970852159116020e08759 -r295ae63db251a5b3006c39e4364dd8576e4f4427
Binary files differ
Index: utils/jalviewjs/eclipse/unused_dropins/net.sf.j2s.core-3.2.4-FOR_4.13.jar
===================================================================
diff -u -N -r438e8852c14561ff835970852159116020e08759 -r295ae63db251a5b3006c39e4364dd8576e4f4427
Binary files differ