diff --git a/independent-projects/bootstrap/core/src/main/java/io/quarkus/bootstrap/resolver/BootstrapAppModelResolver.java b/independent-projects/bootstrap/core/src/main/java/io/quarkus/bootstrap/resolver/BootstrapAppModelResolver.java
index e3e3f40a08350..62a063bbcc508 100644
--- a/independent-projects/bootstrap/core/src/main/java/io/quarkus/bootstrap/resolver/BootstrapAppModelResolver.java
+++ b/independent-projects/bootstrap/core/src/main/java/io/quarkus/bootstrap/resolver/BootstrapAppModelResolver.java
@@ -192,8 +192,26 @@ public boolean visitLeave(DependencyNode node) {
             child.accept(visitor);
         }
 
+        final ArtifactDescriptorResult appArtifactDescr = mvn.resolveDescriptor(toAetherArtifact(appArtifact));
+        if (managedDeps == null) {
+            managedDeps = appArtifactDescr.getManagedDependencies();
+        } else {
+            final List<Dependency> mergedManagedDeps = new ArrayList<>(managedDeps.size());
+            final Set<AppArtifactKey> mergedKeys = new HashSet<>(managedDeps.size());
+            for (Dependency dep : managedDeps) {
+                mergedKeys.add(getKey(dep.getArtifact()));
+                mergedManagedDeps.add(dep);
+            }
+            for (Dependency dep : appArtifactDescr.getManagedDependencies()) {
+                final Artifact artifact = dep.getArtifact();
+                if (!mergedKeys.contains(getKey(artifact))) {
+                    mergedManagedDeps.add(dep);
+                }
+            }
+            managedDeps = mergedManagedDeps;
+        }
         final List<RemoteRepository> repos = mvn.aggregateRepositories(managedRepos,
-                mvn.newResolutionRepositories(mvn.resolveDescriptor(toAetherArtifact(appArtifact)).getRepositories()));
+                mvn.newResolutionRepositories(appArtifactDescr.getRepositories()));
 
         final DeploymentInjectingDependencyVisitor deploymentInjector = new DeploymentInjectingDependencyVisitor(mvn,
                 managedDeps, repos, appBuilder);
@@ -292,6 +310,11 @@ public void install(AppArtifact appArtifact, Path localPath) throws AppModelReso
                 appArtifact.getType(), appArtifact.getVersion(), Collections.emptyMap(), localPath.toFile()));
     }
 
+    private AppArtifactKey getKey(final Artifact artifact) {
+        return new AppArtifactKey(artifact.getGroupId(), artifact.getArtifactId(),
+                artifact.getClassifier(), artifact.getExtension());
+    }
+
     private String getEarliest(final VersionRangeResult rangeResult) {
         final List<Version> versions = rangeResult.getVersions();
         if (versions.isEmpty()) {
diff --git a/independent-projects/bootstrap/core/src/main/java/io/quarkus/bootstrap/resolver/maven/DeploymentInjectingDependencyVisitor.java b/independent-projects/bootstrap/core/src/main/java/io/quarkus/bootstrap/resolver/maven/DeploymentInjectingDependencyVisitor.java
index 9179365e745e1..aeff975c091f2 100644
--- a/independent-projects/bootstrap/core/src/main/java/io/quarkus/bootstrap/resolver/maven/DeploymentInjectingDependencyVisitor.java
+++ b/independent-projects/bootstrap/core/src/main/java/io/quarkus/bootstrap/resolver/maven/DeploymentInjectingDependencyVisitor.java
@@ -126,7 +126,6 @@ private void processPlatformArtifact(DependencyNode node, Path descriptor) throw
         node.setData(QUARKUS_DEPLOYMENT_ARTIFACT, deploymentArtifact);
         runtimeNodes.add(node);
         Dependency dependency = new Dependency(node.getArtifact(), JavaScopes.COMPILE);
-        managedDeps.add(dependency);
         runtimeExtensionDeps.add(dependency);
         managedDeps.add(new Dependency(deploymentArtifact, JavaScopes.COMPILE));
     }
diff --git a/test-framework/junit5/src/main/java/io/quarkus/test/junit/QuarkusTestExtension.java b/test-framework/junit5/src/main/java/io/quarkus/test/junit/QuarkusTestExtension.java
index 0d2f2491eebd1..96ef48355efe3 100644
--- a/test-framework/junit5/src/main/java/io/quarkus/test/junit/QuarkusTestExtension.java
+++ b/test-framework/junit5/src/main/java/io/quarkus/test/junit/QuarkusTestExtension.java
@@ -9,6 +9,7 @@
 import java.lang.reflect.Constructor;
 import java.lang.reflect.InvocationTargetException;
 import java.lang.reflect.Method;
+import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.Collections;
@@ -106,7 +107,7 @@ private ExtensionState doJavaStart(ExtensionContext context) throws Throwable {
             }
             CuratedApplication curatedApplication = runnerBuilder
                     .setTest(true)
-                    .setProjectRoot(new File("").toPath())
+                    .setProjectRoot(Files.isDirectory(appClassLocation) ? new File("").toPath() : null)
                     .build()
                     .bootstrap();