Index: osgi-platforms/felix/src/main/resources/glassfish/osgi/felix/conf/config.properties
===================================================================
--- osgi-platforms/felix/src/main/resources/glassfish/osgi/felix/conf/config.properties	(revision 44468)
+++ osgi-platforms/felix/src/main/resources/glassfish/osgi/felix/conf/config.properties	(working copy)
@@ -105,17 +105,22 @@
 # overlapping packages, we need to install and start endorsed bundles first. 
 # Then we autostart GlassFish provisioning bundle that takes care of installing and starting rest of the bundles.
 # The reason for using reference scheme is that both Felix and Equinox will not cache the bundle.
-# So, any file system update will take effect on next framework restart without having to
-# clean the OSGi cache.
+# reference scheme is only used for osgi-main.jar. For endorsed bundles,
+# we can't use such a scheme as those bundles need special privileges and Java security manager
+# does not understand reference: scheme which is part of code source URL of any bundle installed using
+# reference protocol.
 # The reason for using installRootURI is to make sure any char like white space is properly encoded.
-glassfish.auto.start=reference:${com.sun.aas.installRootURI}/modules/endorsed/jaxb-api-osgi.jar \
-                     reference:${com.sun.aas.installRootURI}/modules/endorsed/webservices-api-osgi.jar \
-                     reference:${com.sun.aas.installRootURI}/modules/endorsed/javax.annotation.jar \
+glassfish.auto.start=${com.sun.aas.installRootURI}/modules/endorsed/jaxb-api-osgi.jar \
+                     ${com.sun.aas.installRootURI}/modules/endorsed/webservices-api-osgi.jar \
+                     ${com.sun.aas.installRootURI}/modules/endorsed/javax.annotation.jar \
                      reference:${com.sun.aas.installRootURI}/modules/osgi-main.jar
 
 # Following three properties are used by GlassFish provisioning bundle (osgi-main.jar)
 org.jvnet.hk2.osgimain.bundlesDir=${com.sun.aas.installRoot}/modules/
-org.jvnet.hk2.osgimain.excludedSubDirs=autostart/, endorsed/
+
+# Even if we install the endorsed bundles using autostart, we include them here as well,
+# so that any changes them to them is reflected without the need to clean the OSGi cache.
+org.jvnet.hk2.osgimain.excludedSubDirs=autostart/
 org.jvnet.hk2.osgimain.autostartBundles=kernel.jar
 
 # The Felix launcher registers a shutdown hook to cleanly stop the framework
Index: osgi-platforms/equinox/src/main/resources/glassfish/osgi/equinox/configuration/config.ini
===================================================================
--- osgi-platforms/equinox/src/main/resources/glassfish/osgi/equinox/configuration/config.ini	(revision 44468)
+++ osgi-platforms/equinox/src/main/resources/glassfish/osgi/equinox/configuration/config.ini	(working copy)
@@ -83,18 +83,22 @@
 # Then we autostart GlassFish provisioning bundle that takes care of installing and starting rest of the bundles.
 # The reason for using reference scheme is that both Felix and Equinox will not cache the bundle.
 # So, any file system update will take effect on next framework restart without having to
-# clean the OSGi cache.
+# clean the OSGi cache. This scheme is only used for osgi-main.jar. For endorsed bundles,
+# we can't use such a scheme as those bundles need special privileges and Java security manager
+# does not understand reference: scheme which is part of code source URL of any bundle installed using
+# reference protocol.
 # The reason for using installRootURI is to make sure any char like white space is properly encoded.
-glassfish.auto.start=reference:${com.sun.aas.installRootURI}/modules/endorsed/jaxb-api-osgi.jar \
-                     reference:${com.sun.aas.installRootURI}/modules/endorsed/webservices-api-osgi.jar \
-                     reference:${com.sun.aas.installRootURI}/modules/endorsed/javax.annotation.jar \
+glassfish.auto.start=${com.sun.aas.installRootURI}/modules/endorsed/jaxb-api-osgi.jar \
+                     ${com.sun.aas.installRootURI}/modules/endorsed/webservices-api-osgi.jar \
+                     ${com.sun.aas.installRootURI}/modules/endorsed/javax.annotation.jar \
                      reference:${com.sun.aas.installRootURI}/modules/osgi-main.jar
 
 # Following three properties are used by GlassFish provisioning bundle (osgi-main.jar)
 org.jvnet.hk2.osgimain.bundlesDir=${com.sun.aas.installRoot}/modules/
 
-# Since we install the endorsed bundles using autostart, exclude them here.
-org.jvnet.hk2.osgimain.excludedSubDirs=autostart/, endorsed/
+# Even if we install the endorsed bundles using autostart, we include them here as well,
+# so that any changes them to them is reflected without the need to clean the OSGi cache.
+org.jvnet.hk2.osgimain.excludedSubDirs=autostart/
 org.jvnet.hk2.osgimain.autostartBundles=kernel.jar
 
 org.osgi.framework.startlevel.beginning=1