--- rt.equinox.p2/bundles/org.eclipse.equinox.p2.engine/src/org/eclipse/equinox/internal/p2/engine/SimpleProfileRegistry.java

+++ rt.equinox.p2/bundles/org.eclipse.equinox.p2.engine/src/org/eclipse/equinox/internal/p2/engine/SimpleProfileRegistry.java

@@ -7,6 +7,7 @@

  * Contributors: 

  *     IBM Corporation - initial API and implementation

  *     Ericsson AB - ongoing development

+ *     Red Hat, Inc. - Bug 408138

  ******************************************************************************/

 package org.eclipse.equinox.internal.p2.engine;

@@ -38,6 +39,7 @@ import org.xml.sax.SAXException;

 public class SimpleProfileRegistry implements IProfileRegistry, IAgentService {

+	private static final String PROP_IGNORE_USER_CONFIGURATION = "eclipse.ignoreUserConfiguration"; //$NON-NLS-1$

 	private static final String SIMPLE_PROFILE_REGISTRY_INTERNAL = "_simpleProfileRegistry_internal_"; //$NON-NLS-1$

 	private static final String PROFILE_REGISTRY = "profile registry"; //$NON-NLS-1$

 	private static final String PROFILE_PROPERTIES_FILE = "state.properties"; //$NON-NLS-1$

@@ -263,6 +265,14 @@ public class SimpleProfileRegistry implements IProfileRegistry, IAgentService {

 					internalSetProfileStateProperty(profile, profile.getTimestamp(), IProfile.STATE_PROP_SHARED_INSTALL, IProfile.STATE_SHARED_INSTALL_VALUE_NEW);

 					internalSetProfileStateProperty(profile, profile.getTimestamp(), SIMPLE_PROFILE_REGISTRY_INTERNAL + getBaseTimestamp(profile.getProfileId()), getBaseTimestamp(id));

 					agent.registerService(SERVICE_SHARED_INSTALL_NEW_TIMESTAMP, Long.toString(profile.getTimestamp()));

+

+					// this looks like a hack, but:

+					// (1) SimpleConfigurationImpl keeps returning master configuration as long as the property is set

+					// (2) SimpleConfigurationImpl sets the propery after it drops user configuration

+					// therefore dropins reconciliation can't load dropins plugins installed into user configuration

+					// after the user configuration has been dropped.

+					// It is necessary to unset this property.

+					//System.setProperty(PROP_IGNORE_USER_CONFIGURATION, "processed_and_unset"); //$NON-NLS-1$ //$NON-NLS-2$

 				} else {

 					//This is the first time we create the shared profile. Tag it as such and also remember the timestamp of the base

 					internalSetProfileStateProperty(profile, profile.getTimestamp(), IProfile.STATE_PROP_SHARED_INSTALL, IProfile.STATE_SHARED_INSTALL_VALUE_INITIAL);

@@ -279,6 +289,12 @@ public class SimpleProfileRegistry implements IProfileRegistry, IAgentService {

 		if (agent.getService(SERVICE_SHARED_INSTALL_NEW_TIMESTAMP) != null)

 			return false;

+		// if the property is set by OSGI, and there is no new timestamp (because of the previous condition)

+		// ignore current profile. This will happen only once, because SERVICE_SHARED_INSTALL_NEW_TIMESTAMP

+		// is set during profile reset.

+		if ("true".equals(System.getProperty(PROP_IGNORE_USER_CONFIGURATION))){ //$NON-NLS-1$ //$NON-NLS-2$

+			System.setProperty(PROP_IGNORE_USER_CONFIGURATION, "processed_and_unset"); //$NON-NLS-1$ //$NON-NLS-2$

+			return true;}

 		String baseTimestamp = getBaseTimestamp(profile.getProfileId());

 		if (baseTimestamp == null)

 			return false;

--- rt.equinox.p2/bundles/org.eclipse.equinox.p2.reconciler.dropins/src/org/eclipse/equinox/internal/p2/reconciler/dropins/ProfileSynchronizer.java

+++ rt.equinox.p2/bundles/org.eclipse.equinox.p2.reconciler.dropins/src/org/eclipse/equinox/internal/p2/reconciler/dropins/ProfileSynchronizer.java

@@ -570,6 +570,7 @@

 		// get all IUs from all our repos 

 		IQueryResult<IInstallableUnit> allIUs = getAllIUsFromRepos();

+		HashSet<IInstallableUnit> removedFromAllIUs = new HashSet<IInstallableUnit>();

 		for (Iterator<IInstallableUnit> iter = allIUs.iterator(); iter.hasNext();) {

 			final IInstallableUnit iu = iter.next();

 			IInstallableUnit existing = profileIUs.get(iu);

@@ -583,6 +584,7 @@

 				// (and more expensive) way to find this out is to do an IU profile property query.

 				if (two == null) {

 					// the IU is already installed so don't mark it as a dropin now - see bug 404619.

+					removedFromAllIUs.add(iu);

 					iter.remove();

 					continue;

 				}

@@ -625,7 +627,7 @@

 			}

 			// if the IU from the profile is in the "all available" list, then it is already added

 			// otherwise if it isn't in the repo then we have to remove it from the profile.

-			if (!all.contains(iu))

+			if (!all.contains(iu) && !removedFromAllIUs.contains(iu))

 				toRemove.add(iu);

 		}

@@ -799,8 +801,8 @@

 			IStatus installerPlanStatus = engine.perform(plan.getInstallerPlan(), phaseSet, monitor);

 			if (!installerPlanStatus.isOK())

 				return installerPlanStatus;

-

-			applyConfiguration(true);

+			if (isReconciliationApplicationRunning())

+				applyConfiguration(true);

 		}

 		return engine.perform(plan, phaseSet, monitor);

 	}