diff --git a/build/org.eclipse.cdt.managedbuilder.core.tests/META-INF/MANIFEST.MF b/build/org.eclipse.cdt.managedbuilder.core.tests/META-INF/MANIFEST.MF
index 9d06cc089b6..20f9a9c7ca5 100644
--- a/build/org.eclipse.cdt.managedbuilder.core.tests/META-INF/MANIFEST.MF
+++ b/build/org.eclipse.cdt.managedbuilder.core.tests/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: %pluginName
 Bundle-SymbolicName: org.eclipse.cdt.managedbuilder.core.tests; singleton:=true
-Bundle-Version: 8.2.200.qualifier
+Bundle-Version: 8.2.201.qualifier
 Bundle-Activator: org.eclipse.cdt.managedbuilder.testplugin.CTestPlugin
 Bundle-Vendor: %providerName
 Bundle-Localization: plugin
diff --git a/build/org.eclipse.cdt.managedbuilder.core.tests/tests/org/eclipse/cdt/managedbuilder/core/tests/BuildDescriptionModelTests.java b/build/org.eclipse.cdt.managedbuilder.core.tests/tests/org/eclipse/cdt/managedbuilder/core/tests/BuildDescriptionModelTests.java
index ee09c004a19..1c30ea8fc1c 100644
--- a/build/org.eclipse.cdt.managedbuilder.core.tests/tests/org/eclipse/cdt/managedbuilder/core/tests/BuildDescriptionModelTests.java
+++ b/build/org.eclipse.cdt.managedbuilder.core.tests/tests/org/eclipse/cdt/managedbuilder/core/tests/BuildDescriptionModelTests.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2006, 2014 Intel Corporation and others.
+ * Copyright (c) 2006, 2022 Intel Corporation and others.
  *
  * This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License 2.0
@@ -10,6 +10,7 @@
  *
  * Contributors:
  * Intel Corporation - Initial API and implementation
+ * John Dallaway - Accommodate extra flags with internal builder (bug 580286)
  *******************************************************************************/
 package org.eclipse.cdt.managedbuilder.core.tests;
 
@@ -1652,13 +1653,6 @@ public class BuildDescriptionModelTests extends TestCase {
 		type.addResource(tDes.createResource("dir2/h.r"));
 		type.addResource(tDes.createResource("dir2/i.r"));
 
-		type = step.createIOType(false, false, null);
-		type.addResource(tDes.createResource("o1.o"));
-		type.addResource(tDes.createResource("dir3/o2.o"));
-		type.addResource(tDes.createResource("dir4/d/o3.o"));
-
-		//
-		//
 		step = tDes.createStep(null, null);
 
 		type = step.createIOType(true, false, null);
@@ -1755,11 +1749,6 @@ public class BuildDescriptionModelTests extends TestCase {
 		//			type.addResource(tDes.createResource(cName + "/t.o"));
 		//			type.addResource(tDes.createResource(cName + "/y.o"));
 
-		//		type = step.createIOType(true, false, null);
-		type.addResource(tDes.createResource("o1.o"));
-		type.addResource(tDes.createResource("dir3/o2.o"));
-		type.addResource(tDes.createResource("dir4/d/o3.o"));
-
 		type = step.createIOType(false, false, null);
 		type.addResource(tDes.createResource(cName + "/" + artifactName));
 		//
diff --git a/build/org.eclipse.cdt.managedbuilder.core/META-INF/MANIFEST.MF b/build/org.eclipse.cdt.managedbuilder.core/META-INF/MANIFEST.MF
index bb7707b45a0..e53143cd02a 100644
--- a/build/org.eclipse.cdt.managedbuilder.core/META-INF/MANIFEST.MF
+++ b/build/org.eclipse.cdt.managedbuilder.core/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: %pluginName
 Bundle-SymbolicName: org.eclipse.cdt.managedbuilder.core; singleton:=true
-Bundle-Version: 9.4.0.qualifier
+Bundle-Version: 9.4.1.qualifier
 Bundle-Activator: org.eclipse.cdt.managedbuilder.core.ManagedBuilderCorePlugin
 Bundle-Vendor: %providerName
 Bundle-Localization: plugin
diff --git a/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/buildmodel/BuildDescription.java b/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/buildmodel/BuildDescription.java
index 7be81a763d1..f65a621e74e 100644
--- a/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/buildmodel/BuildDescription.java
+++ b/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/buildmodel/BuildDescription.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2006, 2016 Intel Corporation and others.
+ * Copyright (c) 2006, 2022 Intel Corporation and others.
  *
  * This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License 2.0
@@ -12,6 +12,7 @@
  * Intel Corporation - Initial API and implementation
  * IBM Corporation
  * John Dallaway - Handle reduced build step input resource count (bug 366039)
+ * John Dallaway - Accommodate extra flags with internal builder (bug 580286)
  *******************************************************************************/
 package org.eclipse.cdt.managedbuilder.internal.buildmodel;
 
@@ -1523,6 +1524,7 @@ public class BuildDescription implements IBuildDescription {
 		 *  3.  Use the file extensions and the resources in the project
 		 */
 		ITool tool = step.getTool();
+		boolean toolHasExtraFlags = tool.getCommandLinePattern().contains("${EXTRA_FLAGS}"); //$NON-NLS-1$
 		IInputType[] inTypes = tool.getInputTypes();
 		if (inTypes != null && inTypes.length > 0) {
 			for (IInputType type : inTypes) {
@@ -1597,7 +1599,8 @@ public class BuildDescription implements IBuildDescription {
 										if ((var = var.trim()).length() != 0) {
 											if (VAR_USER_OBJS.equals(var)) {
 												String objs[] = getUserObjs(step);
-												if (objs != null && objs.length != 0) {
+												// if there are user objects and they will not be provided as extra flags
+												if ((!toolHasExtraFlags) && (objs != null) && (objs.length != 0)) {
 													if (arg == null)
 														arg = step.createIOType(true, primaryInput, type);
 
diff --git a/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/buildmodel/BuildStep.java b/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/buildmodel/BuildStep.java
index 2cf4bc22a24..08ece5ac4f4 100644
--- a/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/buildmodel/BuildStep.java
+++ b/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/buildmodel/BuildStep.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2006, 2016 Intel Corporation and others.
+ * Copyright (c) 2006, 2022 Intel Corporation and others.
  *
  * This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License 2.0
@@ -10,6 +10,7 @@
  *
  * Contributors:
  * Intel Corporation - Initial API and implementation
+ * John Dallaway - Accommodate extra flags with internal builder (bug 580286)
  *******************************************************************************/
 package org.eclipse.cdt.managedbuilder.internal.buildmodel;
 
@@ -358,6 +359,11 @@ public class BuildStep implements IBuildStep {
 	private String[] getInputResources(IPath cwd, BuildResource[] rcs) {
 		String[] resources = resourcesToStrings(cwd, rcs, null);
 
+		// if the libraries will be provided as extra flags we do not need to add them here
+		if (fTool.getCommandLinePattern().contains("${EXTRA_FLAGS}")) { //$NON_NLS-1$
+			return resources;
+		}
+
 		// also need to get libraries
 		String[] libs = null;
 		IOption[] opts = fTool.getOptions();