--- 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);

 	}

--- rt.equinox.p2/bundles/org.eclipse.equinox.p2.ui.sdk.scheduler/src/org/eclipse/equinox/internal/p2/ui/sdk/scheduler/migration/ImportFromInstallationWizard_c.java.bak	2013-06-10 09:33:20.000000000 +0200

+++ rt.equinox.p2/bundles/org.eclipse.equinox.p2.ui.sdk.scheduler/src/org/eclipse/equinox/internal/p2/ui/sdk/scheduler/migration/ImportFromInstallationWizard_c.java	2013-06-11 15:44:28.654682088 +0200

@@ -144,7 +144,7 @@

 	}

 	public boolean performCancel() {

-		String[] buttons = new String[] {IDialogConstants.YES_LABEL, ProvUIMessages.ImportFromInstallationPag_LATER_BUTTON, IDialogConstants.NO_LABEL};

+		String[] buttons = new String[] {IDialogConstants.YES_LABEL, IDialogConstants.NO_LABEL};

 		MessageDialog dialog = new MessageDialog(getShell(), ProvUIMessages.ImportFromInstallationPage_CONFIRMATION_TITLE, null, ProvUIMessages.ImportFromInstallationPage_CONFIRMATION_DIALOG, MessageDialog.QUESTION, buttons, 2);

 		return rememberCancellationDecision(dialog.open());

--- rt.equinox.p2/bundles/org.eclipse.equinox.p2.ui.sdk.scheduler/src/org/eclipse/equinox/internal/p2/ui/sdk/scheduler/migration/ImportFromInstallationPage_c.java

+++ rt.equinox.p2/bundles/org.eclipse.equinox.p2.ui.sdk.scheduler/src/org/eclipse/equinox/internal/p2/ui/sdk/scheduler/migration/ImportFromInstallationPage_c.java

@@ -15,6 +15,7 @@ package org.eclipse.equinox.internal.p2.ui.sdk.scheduler.migration;

 import java.net.URI;

 import org.eclipse.core.runtime.Platform;

 import org.eclipse.equinox.internal.p2.ui.ProvUI;

+import org.eclipse.equinox.internal.p2.ui.QueryProvider;

 import org.eclipse.equinox.internal.p2.ui.dialogs.ISelectableIUsPage;

 import org.eclipse.equinox.internal.p2.ui.dialogs.ProvisioningOperationWizard;

 import org.eclipse.equinox.internal.p2.ui.model.ProfileElement;

@@ -103,6 +104,12 @@ public class ImportFromInstallationPage_c extends AbstractImportPage_c implement

 				public org.eclipse.equinox.p2.query.IQueryable getQueryable() {

 					return toBeImportedProfile;

 				}

+

+				@Override

+				public int getQueryType() {

+					return QueryProvider.STRICT_INSTALLED_IUS;

+				}

+

 			};

 			element.setQueryable(toBeImportedProfile);

 			input = element;

diff --git a/bundles/org.eclipse.equinox.p2.ui/src/org/eclipse/equinox/internal/p2/ui/QueryProvider.java b/bundles/org.eclipse.equinox.p2.ui/src/org/eclipse/equinox/internal/p2/ui/QueryProvider.java

index 9cb6a53..b758ae7 100644

--- rt.equinox.p2/bundles/org.eclipse.equinox.p2.ui/src/org/eclipse/equinox/internal/p2/ui/QueryProvider.java

+++ rt.equinox.p2/bundles/org.eclipse.equinox.p2.ui/src/org/eclipse/equinox/internal/p2/ui/QueryProvider.java

@@ -43,6 +43,7 @@ public class QueryProvider {

 	public static final int AVAILABLE_UPDATES = 5;

 	public static final int INSTALLED_IUS = 6;

 	public static final int AVAILABLE_ARTIFACTS = 7;

+	public static final int STRICT_INSTALLED_IUS = 8;

 	public QueryProvider(ProvisioningUI ui) {

 		this.ui = ui;

@@ -224,6 +225,31 @@ public class QueryProvider {

 					return null;

 				return new ElementQueryDescriptor(queryable, ArtifactKeyQuery.ALL_KEYS, new Collector<Object>(), new ArtifactKeyWrapper((IArtifactRepository) queryable, element));

+			case STRICT_INSTALLED_IUS :

+				// Querying of IU's.  We are drilling down into the requirements.

+				if (element instanceof IIUElement && context.getShowInstallChildren()) {

+					Collection<IRequirement> reqs = ((IIUElement) element).getRequirements();

+					IExpression[] requirementExpressions = new IExpression[reqs.size()];

+					int i = 0;

+					for (IRequirement req : reqs) {

+						requirementExpressions[i++] = req.getMatches();

+					}

+					IExpressionFactory factory = ExpressionUtil.getFactory();

+					IQuery<IInstallableUnit> meetsAnyRequirementQuery = QueryUtil.createMatchQuery(factory.or(requirementExpressions));

+					IQuery<IInstallableUnit> visibleAsAvailableQuery = policy.getVisibleAvailableIUQuery();

+					//dropins things have no file property

+					IQuery<IInstallableUnit> strictQuery = QueryUtil.createIUPropertyQuery("file.name", null); //$NON-NLS-1$

+					IQuery<IInstallableUnit> createCompoundQuery = QueryUtil.createCompoundQuery(QueryUtil.createCompoundQuery(visibleAsAvailableQuery, meetsAnyRequirementQuery, true), strictQuery, true);

+					return new ElementQueryDescriptor(queryable, createCompoundQuery, new Collector<IInstallableUnit>(), new InstalledIUElementWrapper(queryable, element));

+				}

+

+				profile = ProvUI.getAdapter(element, IProfile.class);

+				if (profile == null)

+					return null;

+				//dropins things have no file property

+				IQuery<IInstallableUnit> installedNotDropinsQuery = QueryUtil.createCompoundQuery(policy.getVisibleInstalledIUQuery(), QueryUtil.createIUPropertyQuery("file.name", null), true);

+				return new ElementQueryDescriptor(profile, installedNotDropinsQuery, new Collector<IInstallableUnit>(), new InstalledIUElementWrapper(profile, element)); //$NON-NLS-1$

+

 			default :

 				return null;

 		}