diff --git a/build/org.eclipse.cdt.managedbuilder.core.tests/plugin.xml b/build/org.eclipse.cdt.managedbuilder.core.tests/plugin.xml
index 3d4ea53d48c..2d145e30ce0 100644
--- a/build/org.eclipse.cdt.managedbuilder.core.tests/plugin.xml
+++ b/build/org.eclipse.cdt.managedbuilder.core.tests/plugin.xml
@@ -4944,21 +4944,23 @@
          <configuration
                id="cdt.test.customOptionCommand.one"
                name="One">
-            <toolChain isSystem="true"
+            <toolChain
                   id="cdt.test.customOptionCommand.Toolchain"
                   isAbstract="false"
-                  name="Tools">
+                  isSystem="true"
+                  name="Tools"
+                  targetTool="cdt.test.customOptionCommand.Tool2">
                 <tool
 		            command="xxx"
-		            id="cdt.test.customOptionCommand.Tool"
+		            id="cdt.test.customOptionCommand.Tool1"
 		            isAbstract="false"
-		            name="Tool"
+		            name="Tool1"
 		            natureFilter="both"
 		            outputFlag="-o">
 		         <optionCategory
 		               id="cdt.test.customOptionCommand.optionCategory1"
 		               name="Test Options"
-		               owner="cdt.test.customOptionCommand.Tool"/>
+		               owner="cdt.test.customOptionCommand.Tool1"/>
 		         <option
 		               category="cdt.test.customOptionCommand.optionCategory1"
 		               command="-opt1="
@@ -4986,6 +4988,178 @@
 		               id="cdt.test.customOptionCommand.option4"
 		               name="Option4"
 		               valueType="string"/>
+                </tool>
+                <tool
+		            command="xxx"
+		            id="cdt.test.customOptionCommand.Tool2"
+		            isAbstract="false"
+		            name="Tool2"
+		            natureFilter="both"
+		            outputFlag="-o">
+		         <optionCategory
+		               id="cdt.test.customOptionCommand.optionCategory2"
+		               name="Test Options"
+		               owner="cdt.test.customOptionCommand.Tool2"/>
+		         <option
+		               category="cdt.test.customOptionCommand.optionCategory2"
+		               command="-optString="
+		               id="cdt.test.customOptionCommand.optionString"
+		               name="OptionString"
+		               commandGenerator="org.eclipse.cdt.managedbuilder.core.tests.CustomOptionCommandGenerator"
+		               valueType="string"/>
+		         <option
+		               category="cdt.test.customOptionCommand.optionCategory2"
+		               command="-optStringList="
+		               id="cdt.test.customOptionCommand.optionStringList"
+		               name="OptionStringList"
+		               commandGenerator="org.eclipse.cdt.managedbuilder.core.tests.CustomOptionCommandGenerator"
+		               valueType="stringList"/>
+		         <option
+                 category="cdt.test.customOptionCommand.optionCategory2"
+                 command="-optBoolean=true"
+                 commandFalse="-optBoolean=false"
+                 commandGenerator="org.eclipse.cdt.managedbuilder.core.tests.CustomOptionCommandGenerator"
+                 id="cdt.test.customOptionCommand.optionBoolean"
+                 name="OptionBoolean"
+                 valueType="boolean"/>
+		         <option
+                 category="cdt.test.customOptionCommand.optionCategory2"
+                 command="-optEnumerated="
+                 commandGenerator="org.eclipse.cdt.managedbuilder.core.tests.CustomOptionCommandGenerator"
+                 id="cdt.test.customOptionCommand.optionEnumerated"
+                 name="OptionEnumerated"
+                 valueType="enumerated">
+              <enumeratedOptionValue
+                    command="-optEnumerated=value1"
+                    id="org.eclipse.cdt.managedbuilder.core.tests.enumeratedOptionValue1"
+                    name="EnumeratedOptionValue1">
+              </enumeratedOptionValue>
+              <enumeratedOptionValue
+                    command="-optEnumerated=value2"
+                    id="org.eclipse.cdt.managedbuilder.core.tests.enumeratedOptionValue2"
+                    name="EnumeratedOptionValue2">
+              </enumeratedOptionValue>
+           </option>
+		         <option
+		               category="cdt.test.customOptionCommand.optionCategory2"
+		               command="-optIncludePath="
+		               id="cdt.test.customOptionCommand.optionIncludePath"
+		               name="OptionIncludePath"
+		               commandGenerator="org.eclipse.cdt.managedbuilder.core.tests.CustomOptionCommandGenerator"
+		               valueType="includePath"/>
+		         <option
+		               category="cdt.test.customOptionCommand.optionCategory2"
+		               command="-optDefinedSymbols="
+		               id="cdt.test.customOptionCommand.optionDefinedSymbols"
+		               name="OptionDefinedSymbols"
+		               commandGenerator="org.eclipse.cdt.managedbuilder.core.tests.CustomOptionCommandGenerator"
+		               valueType="definedSymbols"/>
+		         <option
+		               category="cdt.test.customOptionCommand.optionCategory2"
+		               command="-optLibs="
+		               id="cdt.test.customOptionCommand.optionLibs"
+		               name="OptionLibs"
+		               commandGenerator="org.eclipse.cdt.managedbuilder.core.tests.CustomOptionCommandGenerator"
+		               valueType="libs"/>
+		         <option
+		               category="cdt.test.customOptionCommand.optionCategory2"
+		               command="-optUserObjs="
+		               id="cdt.test.customOptionCommand.optionUserObjs"
+		               name="OptionUserObjs"
+		               commandGenerator="org.eclipse.cdt.managedbuilder.core.tests.CustomOptionCommandGenerator"
+		               valueType="userObjs"/>
+		         <option
+		               category="cdt.test.customOptionCommand.optionCategory2"
+		               command="-optSymbolFiles="
+		               id="cdt.test.customOptionCommand.optionSymbolFiles"
+		               name="OptionSymbolFiles"
+		               commandGenerator="org.eclipse.cdt.managedbuilder.core.tests.CustomOptionCommandGenerator"
+		               valueType="symbolFiles"/>
+		         <option
+		               category="cdt.test.customOptionCommand.optionCategory2"
+		               command="-optIncludeFiles="
+		               id="cdt.test.customOptionCommand.optionIncludeFiles"
+		               name="OptionIncludeFiles"
+		               commandGenerator="org.eclipse.cdt.managedbuilder.core.tests.CustomOptionCommandGenerator"
+		               valueType="includeFiles"/>
+		         <option
+		               category="cdt.test.customOptionCommand.optionCategory2"
+		               command="-optLibPaths="
+		               id="cdt.test.customOptionCommand.optionLibPaths"
+		               name="OptionLibPaths"
+		               commandGenerator="org.eclipse.cdt.managedbuilder.core.tests.CustomOptionCommandGenerator"
+		               valueType="libPaths"/>
+		         <option
+		               category="cdt.test.customOptionCommand.optionCategory2"
+		               command="-optLibFiles="
+		               id="cdt.test.customOptionCommand.optionLibFiles"
+		               name="OptionLibFiles"
+		               commandGenerator="org.eclipse.cdt.managedbuilder.core.tests.CustomOptionCommandGenerator"
+		               valueType="libFiles"/>
+		         <option
+		               category="cdt.test.customOptionCommand.optionCategory2"
+		               command="-optUndefIncludePath="
+		               id="cdt.test.customOptionCommand.optionUndefIncludePath"
+		               name="OptionUndefIncludePath"
+		               commandGenerator="org.eclipse.cdt.managedbuilder.core.tests.CustomOptionCommandGenerator"
+		               valueType="undefIncludePath"/>
+		         <option
+		               category="cdt.test.customOptionCommand.optionCategory2"
+		               command="-optUndefDefinedSymbols="
+		               id="cdt.test.customOptionCommand.optionUndefDefinedSymbols"
+		               name="OptionUndefDefinedSymbols"
+		               commandGenerator="org.eclipse.cdt.managedbuilder.core.tests.CustomOptionCommandGenerator"
+		               valueType="undefDefinedSymbols"/>
+		         <option
+		               category="cdt.test.customOptionCommand.optionCategory2"
+		               command="-optUndefLibPaths="
+		               id="cdt.test.customOptionCommand.optionUndefLibPaths"
+		               name="OptionUndefLibPaths"
+		               commandGenerator="org.eclipse.cdt.managedbuilder.core.tests.CustomOptionCommandGenerator"
+		               valueType="undefLibPaths"/>
+		         <option
+		               category="cdt.test.customOptionCommand.optionCategory2"
+		               command="-optUndefLibFiles="
+		               id="cdt.test.customOptionCommand.optionUndefLibFiles"
+		               name="OptionUndefLibFiles"
+		               commandGenerator="org.eclipse.cdt.managedbuilder.core.tests.CustomOptionCommandGenerator"
+		               valueType="undefLibFiles"/>
+		         <option
+		               category="cdt.test.customOptionCommand.optionCategory2"
+		               command="-optUndefIncludeFiles="
+		               id="cdt.test.customOptionCommand.optionUndefIncludeFiles"
+		               name="OptionUndefIncludeFiles"
+		               commandGenerator="org.eclipse.cdt.managedbuilder.core.tests.CustomOptionCommandGenerator"
+		               valueType="undefIncludeFiles"/>
+		         <option
+		               category="cdt.test.customOptionCommand.optionCategory2"
+		               command="-optUndefSymbolFiles="
+		               id="cdt.test.customOptionCommand.optionUndefSymbolFiles"
+		               name="OptionUndefSymbolFiles"
+		               commandGenerator="org.eclipse.cdt.managedbuilder.core.tests.CustomOptionCommandGenerator"
+		               valueType="undefSymbolFiles"/>
+		         <option
+                 category="cdt.test.customOptionCommand.optionCategory2"
+                 command="-optTree="
+                 commandGenerator="org.eclipse.cdt.managedbuilder.core.tests.CustomOptionCommandGenerator"
+                 id="cdt.test.customOptionCommand.optionTree"
+                 name="OptionTree"
+                 valueType="tree">
+              <treeOptionRoot
+                    id="org.eclipse.cdt.managedbuilder.core.tests.treeOptionRoot1"
+                    name="org.eclipse.cdt.managedbuilder.core.tests.treeOptionRoot1">
+                 <treeOption
+                       command="-optTree=value1"
+                       id="org.eclipse.cdt.managedbuilder.core.tests.treeOption1"
+                       name="TreeOption1">
+                 </treeOption>
+                 <treeOption
+                       command="-optTree=value2"
+                       id="org.eclipse.cdt.managedbuilder.core.tests.treeOption2"
+                       name="TreeOption2">
+                 </treeOption>
+              </treeOptionRoot>
+           </option>
                 </tool>
 				<builder
 				    id="cdt.test.customOptionCommand.builder"
diff --git a/build/org.eclipse.cdt.managedbuilder.core.tests/tests/org/eclipse/cdt/managedbuilder/core/tests/CustomOptionCommandGenerator2.java b/build/org.eclipse.cdt.managedbuilder.core.tests/tests/org/eclipse/cdt/managedbuilder/core/tests/CustomOptionCommandGenerator2.java
new file mode 100644
index 00000000000..2d76300e07b
--- /dev/null
+++ b/build/org.eclipse.cdt.managedbuilder.core.tests/tests/org/eclipse/cdt/managedbuilder/core/tests/CustomOptionCommandGenerator2.java
@@ -0,0 +1,34 @@
+package org.eclipse.cdt.managedbuilder.core.tests;
+
+import org.eclipse.cdt.managedbuilder.core.BuildException;
+import org.eclipse.cdt.managedbuilder.core.IOption;
+import org.eclipse.cdt.utils.cdtvariables.IVariableSubstitutor;
+
+public class CustomOptionCommandGenerator2 extends CustomOptionCommandGenerator {
+
+	public CustomOptionCommandGenerator2() {
+	}
+
+	@Override
+	public String generateCommand(IOption option, IVariableSubstitutor macroSubstitutor) {
+		String command = super.generateCommand(option, macroSubstitutor);
+		if (command == null) {
+			try {
+				switch (option.getValueType()) {
+				case IOption.BOOLEAN:
+					return option.getBooleanValue() ? option.getCommand() : option.getCommandFalse();
+				case IOption.ENUMERATED:
+					return option.getEnumCommand(option.getSelectedEnum());
+				case IOption.TREE:
+					return option.getCommand(option.getStringValue());
+				default:
+					return option.getCommand() + option.getValue();
+				}
+			} catch (BuildException e) {
+				return "CustomOptionCommandGenerator2-error";
+			}
+		}
+		return command;
+	}
+
+}
diff --git a/build/org.eclipse.cdt.managedbuilder.core.tests/tests/org/eclipse/cdt/managedbuilder/core/tests/ManagedCommandLineGeneratorTest.java b/build/org.eclipse.cdt.managedbuilder.core.tests/tests/org/eclipse/cdt/managedbuilder/core/tests/ManagedCommandLineGeneratorTest.java
index 7d559a3222d..e661cb1f668 100644
--- a/build/org.eclipse.cdt.managedbuilder.core.tests/tests/org/eclipse/cdt/managedbuilder/core/tests/ManagedCommandLineGeneratorTest.java
+++ b/build/org.eclipse.cdt.managedbuilder.core.tests/tests/org/eclipse/cdt/managedbuilder/core/tests/ManagedCommandLineGeneratorTest.java
@@ -15,6 +15,7 @@
 package org.eclipse.cdt.managedbuilder.core.tests;
 
 import java.util.ArrayList;
+import java.util.Arrays;
 
 import org.eclipse.cdt.managedbuilder.core.IConfiguration;
 import org.eclipse.cdt.managedbuilder.core.IManagedBuildInfo;
@@ -194,8 +195,8 @@ public class ManagedCommandLineGeneratorTest extends TestCase {
 					"cdt.test.customOptionCommand.ProjectType");
 			IManagedBuildInfo info = ManagedBuildManager.getBuildInfo(project);
 			IConfiguration config = info.getDefaultConfiguration();
-			ITool[] tools = config.getToolsBySuperClassId("cdt.test.customOptionCommand.Tool");
-			assertEquals(tools.length, 1);
+			ITool[] tools = config.getToolsBySuperClassId("cdt.test.customOptionCommand.Tool1");
+			assertEquals(1, tools.length);
 
 			ITool tool = tools[0];
 
@@ -229,6 +230,124 @@ public class ManagedCommandLineGeneratorTest extends TestCase {
 		}
 	}
 
+	public final void testCustomOptionCommandGenerator2() {
+		try {
+			IProject project = ManagedBuildTestHelper.createProject("COCG2", null, (IPath) null,
+					"cdt.test.customOptionCommand.ProjectType");
+			IManagedBuildInfo info = ManagedBuildManager.getBuildInfo(project);
+			IConfiguration config = info.getDefaultConfiguration();
+
+			ITool[] tools = config.getToolsBySuperClassId("cdt.test.customOptionCommand.Tool2");
+			assertEquals(1, tools.length);
+
+			ITool tool = tools[0];
+
+			IOption optionString = tool.getOptionBySuperClassId("cdt.test.customOptionCommand.optionString");
+			IOption optionStringList = tool.getOptionBySuperClassId("cdt.test.customOptionCommand.optionStringList");
+			IOption optionBoolean = tool.getOptionBySuperClassId("cdt.test.customOptionCommand.optionBoolean");
+			IOption optionEnumerated = tool.getOptionBySuperClassId("cdt.test.customOptionCommand.optionEnumerated");
+			IOption optionIncludePath = tool.getOptionBySuperClassId("cdt.test.customOptionCommand.optionIncludePath");
+			IOption optionDefinedSymbols = tool
+					.getOptionBySuperClassId("cdt.test.customOptionCommand.optionDefinedSymbols");
+			IOption optionLibs = tool.getOptionBySuperClassId("cdt.test.customOptionCommand.optionLibs");
+			IOption optionUserObjs = tool.getOptionBySuperClassId("cdt.test.customOptionCommand.optionUserObjs");
+			IOption optionSymbolFiles = tool.getOptionBySuperClassId("cdt.test.customOptionCommand.optionSymbolFiles");
+			IOption optionIncludeFiles = tool
+					.getOptionBySuperClassId("cdt.test.customOptionCommand.optionIncludeFiles");
+			IOption optionLibPaths = tool.getOptionBySuperClassId("cdt.test.customOptionCommand.optionLibPaths");
+			IOption optionLibFiles = tool.getOptionBySuperClassId("cdt.test.customOptionCommand.optionLibFiles");
+			IOption optionUndefIncludePath = tool
+					.getOptionBySuperClassId("cdt.test.customOptionCommand.optionUndefIncludePath");
+			IOption optionUndefDefinedSymbols = tool
+					.getOptionBySuperClassId("cdt.test.customOptionCommand.optionUndefDefinedSymbols");
+			IOption optionUndefLibPaths = tool
+					.getOptionBySuperClassId("cdt.test.customOptionCommand.optionUndefLibPaths");
+			IOption optionUndefLibFiles = tool
+					.getOptionBySuperClassId("cdt.test.customOptionCommand.optionUndefLibFiles");
+			IOption optionUndefIncludeFiles = tool
+					.getOptionBySuperClassId("cdt.test.customOptionCommand.optionUndefIncludeFiles");
+			IOption optionUndefSymbolFiles = tool
+					.getOptionBySuperClassId("cdt.test.customOptionCommand.optionUndefSymbolFiles");
+			IOption optionTree = tool.getOptionBySuperClassId("cdt.test.customOptionCommand.optionTree");
+
+			assertTrue(optionString.getCommandGenerator() instanceof CustomOptionCommandGenerator);
+			assertTrue(optionStringList.getCommandGenerator() instanceof CustomOptionCommandGenerator);
+			assertTrue(optionBoolean.getCommandGenerator() instanceof CustomOptionCommandGenerator);
+			assertTrue(optionEnumerated.getCommandGenerator() instanceof CustomOptionCommandGenerator);
+			assertTrue(optionIncludePath.getCommandGenerator() instanceof CustomOptionCommandGenerator);
+			assertTrue(optionDefinedSymbols.getCommandGenerator() instanceof CustomOptionCommandGenerator);
+			assertTrue(optionLibs.getCommandGenerator() instanceof CustomOptionCommandGenerator);
+			assertTrue(optionUserObjs.getCommandGenerator() instanceof CustomOptionCommandGenerator);
+			assertTrue(optionSymbolFiles.getCommandGenerator() instanceof CustomOptionCommandGenerator);
+			assertTrue(optionIncludeFiles.getCommandGenerator() instanceof CustomOptionCommandGenerator);
+			assertTrue(optionLibPaths.getCommandGenerator() instanceof CustomOptionCommandGenerator);
+			assertTrue(optionLibFiles.getCommandGenerator() instanceof CustomOptionCommandGenerator);
+			assertTrue(optionUndefIncludePath.getCommandGenerator() instanceof CustomOptionCommandGenerator);
+			assertTrue(optionUndefDefinedSymbols.getCommandGenerator() instanceof CustomOptionCommandGenerator);
+			assertTrue(optionUndefLibPaths.getCommandGenerator() instanceof CustomOptionCommandGenerator);
+			assertTrue(optionUndefLibFiles.getCommandGenerator() instanceof CustomOptionCommandGenerator);
+			assertTrue(optionUndefIncludeFiles.getCommandGenerator() instanceof CustomOptionCommandGenerator);
+			assertTrue(optionUndefSymbolFiles.getCommandGenerator() instanceof CustomOptionCommandGenerator);
+			assertTrue(optionTree.getCommandGenerator() instanceof CustomOptionCommandGenerator);
+
+			optionString = config.setOption(tool, optionString, "${ProjName}");
+			optionStringList = config.setOption(tool, optionStringList, new String[] { "val1", "${ProjName}" });
+			optionBoolean = config.setOption(tool, optionBoolean, true);
+			optionEnumerated = config.setOption(tool, optionEnumerated,
+					"org.eclipse.cdt.managedbuilder.core.tests.enumeratedOptionValue2");
+			optionIncludePath = config.setOption(tool, optionIncludePath, new String[] { "val2", "${ProjName}" });
+			optionDefinedSymbols = config.setOption(tool, optionDefinedSymbols, new String[] { "val3", "${ProjName}" });
+			optionLibs = config.setOption(tool, optionLibs, new String[] { "val4", "${ProjName}" });
+			optionUserObjs = config.setOption(tool, optionUserObjs, new String[] { "val5", "${ProjName}" });
+			optionSymbolFiles = config.setOption(tool, optionSymbolFiles, new String[] { "val6", "${ProjName}" });
+			optionIncludeFiles = config.setOption(tool, optionIncludeFiles, new String[] { "val7", "${ProjName}" });
+			optionLibPaths = config.setOption(tool, optionLibPaths, new String[] { "val8", "${ProjName}" });
+			optionLibFiles = config.setOption(tool, optionLibFiles, new String[] { "val9", "${ProjName}" });
+			optionUndefIncludePath = config.setOption(tool, optionUndefIncludePath,
+					new String[] { "val10", "${ProjName}" });
+			optionUndefDefinedSymbols = config.setOption(tool, optionUndefDefinedSymbols,
+					new String[] { "val11", "${ProjName}" });
+			optionUndefLibPaths = config.setOption(tool, optionUndefLibPaths, new String[] { "val12", "${ProjName}" });
+			optionUndefLibFiles = config.setOption(tool, optionUndefLibFiles, new String[] { "val13", "${ProjName}" });
+			optionUndefIncludeFiles = config.setOption(tool, optionUndefIncludeFiles,
+					new String[] { "val14", "${ProjName}" });
+			optionUndefSymbolFiles = config.setOption(tool, optionUndefSymbolFiles,
+					new String[] { "val15", "${ProjName}" });
+			optionTree = config.setOption(tool, optionTree, "org.eclipse.cdt.managedbuilder.core.tests.treeOption2");
+
+			String command = tool.getToolCommandFlagsString(null, null);
+			assertEquals(String.join(" ", "-optString=COCG2", //
+					"-optStringList=\"val1;COCG2;\"", //
+					"-optBoolean=true", //
+					"-optEnumerated=value2", //
+					"-optIncludePath=\"val2;COCG2;\"", //
+					"-optDefinedSymbols=\"val3;COCG2;\"", //
+					"-optSymbolFiles=\"val6;COCG2;\"", //
+					"-optIncludeFiles=\"val7;COCG2;\"", //
+					"-optLibPaths=\"val8;COCG2;\"", //
+					"-optLibFiles=\"val9;COCG2;\"", //
+					"-optUndefIncludePath=\"val10;COCG2;\"", //
+					"-optUndefDefinedSymbols=\"val11;COCG2;\"", //
+					"-optUndefLibPaths=\"val12;COCG2;\"", //
+					"-optUndefLibFiles=\"val13;COCG2;\"", //
+					"-optUndefIncludeFiles=\"val14;COCG2;\"", //
+					"-optUndefSymbolFiles=\"val15;COCG2;\"", //
+					"-optTree=value2"), //
+					command);
+
+			String[] libs = config.getLibs(config.getArtifactExtension());
+			assertEquals(Arrays.asList("-optLibs=\"val4;COCG2;\"").toString(), Arrays.asList(libs).toString());
+
+			String[] userObjs = config.getUserObjects(config.getArtifactExtension());
+			assertEquals(Arrays.asList("-optUserObjs=\"val5;COCG2;\"").toString(), Arrays.asList(userObjs).toString());
+
+			ManagedBuildTestHelper.removeProject("COCG2");
+		} catch (Exception e) {
+			e.printStackTrace();
+			fail("Test failed on project creation: " + e.getLocalizedMessage());
+		}
+	}
+
 	public final void testDollarValue() {
 		try {
 			IProject project = ManagedBuildTestHelper.createProject("CDV", null, (IPath) null,
diff --git a/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/core/Configuration.java b/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/core/Configuration.java
index 81d6821d0eb..bf4b762ffab 100644
--- a/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/core/Configuration.java
+++ b/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/core/Configuration.java
@@ -30,6 +30,7 @@ import java.util.Vector;
 import org.eclipse.cdt.build.core.scannerconfig.ICfgScannerConfigBuilderInfo2Set;
 import org.eclipse.cdt.build.internal.core.scannerconfig.CfgDiscoveredPathManager.PathInfoCache;
 import org.eclipse.cdt.core.ErrorParserManager;
+import org.eclipse.cdt.core.cdtvariables.CdtVariableException;
 import org.eclipse.cdt.core.settings.model.CSourceEntry;
 import org.eclipse.cdt.core.settings.model.ICConfigurationDescription;
 import org.eclipse.cdt.core.settings.model.ICExternalSetting;
@@ -65,6 +66,7 @@ import org.eclipse.cdt.managedbuilder.core.IManagedOptionValueHandler;
 import org.eclipse.cdt.managedbuilder.core.IManagedProject;
 import org.eclipse.cdt.managedbuilder.core.IOption;
 import org.eclipse.cdt.managedbuilder.core.IOptionApplicability;
+import org.eclipse.cdt.managedbuilder.core.IOptionCommandGenerator;
 import org.eclipse.cdt.managedbuilder.core.IProjectType;
 import org.eclipse.cdt.managedbuilder.core.IResourceConfiguration;
 import org.eclipse.cdt.managedbuilder.core.IResourceInfo;
@@ -77,11 +79,15 @@ import org.eclipse.cdt.managedbuilder.envvar.IConfigurationEnvironmentVariableSu
 import org.eclipse.cdt.managedbuilder.internal.dataprovider.BuildConfigurationData;
 import org.eclipse.cdt.managedbuilder.internal.enablement.OptionEnablementExpression;
 import org.eclipse.cdt.managedbuilder.internal.macros.BuildMacroProvider;
+import org.eclipse.cdt.managedbuilder.internal.macros.BuildfileMacroSubstitutor;
 import org.eclipse.cdt.managedbuilder.internal.macros.FileContextData;
+import org.eclipse.cdt.managedbuilder.internal.macros.IMacroContextInfo;
+import org.eclipse.cdt.managedbuilder.internal.macros.IMacroContextInfoProvider;
 import org.eclipse.cdt.managedbuilder.internal.macros.OptionContextData;
 import org.eclipse.cdt.managedbuilder.macros.BuildMacroException;
 import org.eclipse.cdt.managedbuilder.macros.IBuildMacroProvider;
 import org.eclipse.cdt.managedbuilder.macros.IConfigurationBuildMacroSupplier;
+import org.eclipse.cdt.utils.cdtvariables.SupplierBasedCdtVariableSubstitutor;
 import org.eclipse.core.resources.IFile;
 import org.eclipse.core.resources.IResource;
 import org.eclipse.core.resources.IResourceDelta;
@@ -95,6 +101,7 @@ import org.osgi.framework.Version;
 public class Configuration extends BuildObject implements IConfiguration, IBuildPropertiesRestriction,
 		IBuildPropertyChangeListener, IRealBuildObjectAssociation {
 
+	private static final String WHITE_SPACE = " "; //$NON-NLS-1$
 	private static final String EMPTY_STRING = ""; //$NON-NLS-1$
 	private static final String EMPTY_CFG_ID = "org.eclipse.cdt.build.core.emptycfg"; //$NON-NLS-1$
 	private static final String LANGUAGE_SETTINGS_PROVIDER_DELIMITER = ";"; //$NON-NLS-1$
@@ -2600,25 +2607,51 @@ public class Configuration extends BuildObject implements IConfiguration, IBuild
 				IOption option = opts[i];
 				try {
 					if (option.getValueType() == IOption.OBJECTS) {
-						String unresolved[] = option.getUserObjects();
-						if (unresolved != null && unresolved.length > 0) {
-							for (int k = 0; k < unresolved.length; k++) {
-								try {
-									String resolved[] = ManagedBuildManager.getBuildMacroProvider()
-											.resolveStringListValueToMakefileFormat(unresolved[k], "", //$NON-NLS-1$
-													" ", //$NON-NLS-1$
-													IBuildMacroProvider.CONTEXT_OPTION,
-													new OptionContextData(option, tool));
-									if (resolved != null && resolved.length > 0)
-										objs.addAll(Arrays.asList(resolved));
-								} catch (BuildMacroException e) {
-									// TODO: report error
-									continue;
+						// check to see if the option has an applicability calculator
+						IOptionApplicability applicabilityCalculator = option.getApplicabilityCalculator();
+
+						if (applicabilityCalculator == null
+								|| applicabilityCalculator.isOptionUsedInCommandLine(this, tool, option)) {
+							boolean generateDefaultCommand = true;
+							IOptionCommandGenerator commandGenerator = option.getCommandGenerator();
+							if (commandGenerator != null) {
+								SupplierBasedCdtVariableSubstitutor macroSubstitutor = new BuildfileMacroSubstitutor(
+										null, EMPTY_STRING, WHITE_SPACE);
+								IMacroContextInfoProvider provider = BuildMacroProvider.getDefault();
+								IMacroContextInfo info = provider.getMacroContextInfo(BuildMacroProvider.CONTEXT_OPTION,
+										new OptionContextData(option, tool));
+								if (info != null) {
+									macroSubstitutor.setMacroContextInfo(info);
+									String command = commandGenerator.generateCommand(option, macroSubstitutor);
+									if (command != null) {
+										objs.add(command);
+										generateDefaultCommand = false;
+									}
+								}
+							}
+
+							if (generateDefaultCommand) {
+								String unresolved[] = option.getUserObjects();
+								if (unresolved != null && unresolved.length > 0) {
+									for (int k = 0; k < unresolved.length; k++) {
+										try {
+											String resolved[] = ManagedBuildManager.getBuildMacroProvider()
+													.resolveStringListValueToMakefileFormat(unresolved[k], "", //$NON-NLS-1$
+															" ", //$NON-NLS-1$
+															IBuildMacroProvider.CONTEXT_OPTION,
+															new OptionContextData(option, tool));
+											if (resolved != null && resolved.length > 0)
+												objs.addAll(Arrays.asList(resolved));
+										} catch (BuildMacroException e) {
+											// TODO: report error
+											continue;
+										}
+									}
 								}
 							}
 						}
 					}
-				} catch (BuildException e) {
+				} catch (BuildException | CdtVariableException e) {
 					// TODO: report error
 					continue;
 				}
@@ -2643,35 +2676,54 @@ public class Configuration extends BuildObject implements IConfiguration, IBuild
 					if (option.getValueType() == IOption.LIBRARIES) {
 
 						// check to see if the option has an applicability calculator
-						IOptionApplicability applicabilitytCalculator = option.getApplicabilityCalculator();
+						IOptionApplicability applicabilityCalculator = option.getApplicabilityCalculator();
 
-						if (applicabilitytCalculator == null
-								|| applicabilitytCalculator.isOptionUsedInCommandLine(this, tool, option)) {
-							String command = option.getCommand();
-							String[] allLibs = option.getLibraries();
-							for (int j = 0; j < allLibs.length; j++) {
-								try {
-									String resolved[] = ManagedBuildManager.getBuildMacroProvider()
-											.resolveStringListValueToMakefileFormat(allLibs[j], "", //$NON-NLS-1$
-													" ", //$NON-NLS-1$
-													IBuildMacroProvider.CONTEXT_OPTION,
-													new OptionContextData(option, tool));
-									if (resolved != null && resolved.length > 0) {
-										for (int k = 0; k < resolved.length; k++) {
-											String string = resolved[k];
-											if (string.length() > 0)
-												libs.add(command + string);
-										}
+						if (applicabilityCalculator == null
+								|| applicabilityCalculator.isOptionUsedInCommandLine(this, tool, option)) {
+							boolean generateDefaultCommand = true;
+							IOptionCommandGenerator commandGenerator = option.getCommandGenerator();
+							if (commandGenerator != null) {
+								SupplierBasedCdtVariableSubstitutor macroSubstitutor = new BuildfileMacroSubstitutor(
+										null, EMPTY_STRING, WHITE_SPACE);
+								IMacroContextInfoProvider provider = BuildMacroProvider.getDefault();
+								IMacroContextInfo info = provider.getMacroContextInfo(BuildMacroProvider.CONTEXT_OPTION,
+										new OptionContextData(option, tool));
+								if (info != null) {
+									macroSubstitutor.setMacroContextInfo(info);
+									String command = commandGenerator.generateCommand(option, macroSubstitutor);
+									if (command != null) {
+										libs.add(command);
+										generateDefaultCommand = false;
 									}
-								} catch (BuildMacroException e) {
-									// TODO: report error
-									continue;
 								}
+							}
 
+							if (generateDefaultCommand) {
+								String command = option.getCommand();
+								String[] allLibs = option.getLibraries();
+								for (int j = 0; j < allLibs.length; j++) {
+									try {
+										String resolved[] = ManagedBuildManager.getBuildMacroProvider()
+												.resolveStringListValueToMakefileFormat(allLibs[j], " ", //$NON-NLS-1$
+														" ", //$NON-NLS-1$
+														IBuildMacroProvider.CONTEXT_OPTION,
+														new OptionContextData(option, tool));
+										if (resolved != null && resolved.length > 0) {
+											for (int k = 0; k < resolved.length; k++) {
+												String string = resolved[k];
+												if (string.length() > 0)
+													libs.add(command + string);
+											}
+										}
+									} catch (BuildMacroException e) {
+										// TODO: report error
+										continue;
+									}
+								}
 							}
 						}
 					}
-				} catch (BuildException e) {
+				} catch (BuildException | CdtVariableException e) {
 					// TODO: report error
 					continue;
 				}
diff --git a/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/core/Tool.java b/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/core/Tool.java
index 894a6c9eea6..0fd5e1076c4 100644
--- a/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/core/Tool.java
+++ b/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/core/Tool.java
@@ -2655,15 +2655,37 @@ public class Tool extends HoldsOptions
 					boolean generateDefaultCommand = true;
 					IOptionCommandGenerator commandGenerator = option.getCommandGenerator();
 					if (commandGenerator != null) {
-						IMacroContextInfo info = provider.getMacroContextInfo(BuildMacroProvider.CONTEXT_FILE,
-								new FileContextData(inputFileLocation, outputFileLocation, option, this));
-						if (info != null) {
-							macroSubstitutor.setMacroContextInfo(info);
-							String command = commandGenerator.generateCommand(option, macroSubstitutor);
-							if (command != null) {
-								sb.append(command);
-								generateDefaultCommand = false;
+						switch (option.getValueType()) {
+						case IOption.BOOLEAN:
+						case IOption.ENUMERATED:
+						case IOption.TREE:
+						case IOption.STRING:
+						case IOption.STRING_LIST:
+						case IOption.INCLUDE_FILES:
+						case IOption.INCLUDE_PATH:
+						case IOption.LIBRARY_PATHS:
+						case IOption.LIBRARY_FILES:
+						case IOption.MACRO_FILES:
+						case IOption.UNDEF_INCLUDE_FILES:
+						case IOption.UNDEF_INCLUDE_PATH:
+						case IOption.UNDEF_LIBRARY_PATHS:
+						case IOption.UNDEF_LIBRARY_FILES:
+						case IOption.UNDEF_MACRO_FILES:
+						case IOption.PREPROCESSOR_SYMBOLS:
+						case IOption.UNDEF_PREPROCESSOR_SYMBOLS:
+							IMacroContextInfo info = provider.getMacroContextInfo(BuildMacroProvider.CONTEXT_FILE,
+									new FileContextData(inputFileLocation, outputFileLocation, option, this));
+							if (info != null) {
+								macroSubstitutor.setMacroContextInfo(info);
+								String command = commandGenerator.generateCommand(option, macroSubstitutor);
+								if (command != null) {
+									sb.append(command);
+									generateDefaultCommand = false;
+								}
 							}
+							break;
+						default:
+							break;
 						}
 					}
 					if (generateDefaultCommand) {