testOutputDir = tests
utilsDir = utils
-buildPropertiesFile = .build_properties
+build_properties_file = .build_properties
application_codebase = *.jalview.org
mainClass = jalview.bin.Jalview
shadowJarMainClass = jalview.bin.Launcher
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
-jalviewjs_swingjs_zip = SwingJS-site.zip
-jalviewjs_libjs_dir = libjs
-jalviewjs_resource_dir = resources
-jalviewjs_site_resource_dir = site-resources
-jalviewjs_site_dir = site
-jalviewjs_j2s_subdir = swingjs/j2s
-jalviewjs_j2s_settings_file = dot_j2s
+jalviewjs_eclipse_dropins_dir = utils/jalviewjs/eclipse/dropins
+jalviewjs_swingjs_zip = swingjs/SwingJS-site.zip
+jalviewjs_j2s_plugin = swingjs/net.sf.j2s.core.jar
+jalviewjs_libjs_dir = utils/jalviewjs/libjs
+jalviewjs_site_resource_dir = utils/jalviewjs/site-resources
+jalviewjs_classlists_dir = utils/jalviewjs/classlists
jalviewjs_j2s_settings = .j2s
-#jalviewjs_eclipse_workspace = ../tmp/eclipse-workspace
+#jalviewjs_eclipse_workspace = ~/tmp/eclipse-workspace
+# these 3 files/dirs found in build/jalviewjs
+jalviewjs_eclipse_tmp_dropins_dir = eclipse_dropins
jalviewjs_eclipse_workspace_location_file = eclipse_workspace_location
+jalviewjs_site_dir = site
+# these dirs are subdirs of the site dir
+jalviewjs_swingjs_subdir = swingjs
+jalviewjs_j2s_subdir = swingjs/j2s
+jalviewjs_js_subdir = swingjs/js
#jalviewjs_eclipseBuildArg = build
-jalviewjs_eclipseBuildArg = cleanBuild
+jalviewjs_eclipse_build_arg = cleanBuild
jalviewjs_server_port = 9001
jalviewjs_server_wait = 30
jalviewjs_server_resource = /jalview_bin_Jalview.html
#output will be comma-separated: called method,caller class
#j2s.prop.j2s.log.all.calls=true
-jalviewjs_j2s_stdout = j2s-transpile.out
+jalviewjs_j2s_transpile_stdout = j2s-transpile.out
#jalviewjs_j2s_stderr = j2s-transpile.err # all going into out
jalviewjs_j2s_to_console = true
+jalviewjs_j2s_closure_stdout = j2s-closure.out
-
+testp=gradle.properties