diff --git a/build/org.eclipse.cdt.managedbuilder.core.tests/plugin.xml b/build/org.eclipse.cdt.managedbuilder.core.tests/plugin.xml
index 4611ce2a8d0..2110f4ad174 100644
--- a/build/org.eclipse.cdt.managedbuilder.core.tests/plugin.xml
+++ b/build/org.eclipse.cdt.managedbuilder.core.tests/plugin.xml
@@ -9601,6 +9601,21 @@
                   resourceFilter="all"
                   valueType="string">
             </option>
+            <option
+                  command="-not-excluded-from-scanner-discovery"
+                  id="cdt.managedbuilder.lsp.tests.option.not-excluded-sd"
+                  isAbstract="false"
+                  resourceFilter="all"
+                  valueType="string">
+            </option>
+            <option
+                  command="-is-excluded-from-scanner-discovery"
+                  id="cdt.managedbuilder.lsp.tests.option.is-excluded-sd"
+                  isAbstract="false"
+                  resourceFilter="all"
+                  excludeFromScannerDiscovery="true"
+                  valueType="string">
+            </option>
             <option
                   command="-bool-option"
                   defaultValue="true"
diff --git a/build/org.eclipse.cdt.managedbuilder.core.tests/tests/org/eclipse/cdt/managedbuilder/core/tests/ManagedBuildCoreTests.java b/build/org.eclipse.cdt.managedbuilder.core.tests/tests/org/eclipse/cdt/managedbuilder/core/tests/ManagedBuildCoreTests.java
index 3825f848f80..720549ade59 100644
--- a/build/org.eclipse.cdt.managedbuilder.core.tests/tests/org/eclipse/cdt/managedbuilder/core/tests/ManagedBuildCoreTests.java
+++ b/build/org.eclipse.cdt.managedbuilder.core.tests/tests/org/eclipse/cdt/managedbuilder/core/tests/ManagedBuildCoreTests.java
@@ -34,9 +34,6 @@
 import org.eclipse.core.runtime.IConfigurationElement;
 import org.junit.Assert;
 
-import junit.framework.Test;
-import junit.framework.TestSuite;
-
 public class ManagedBuildCoreTests extends BaseTestCase {
 	private static IProjectType exeType;
 	private static IProjectType libType;
@@ -46,14 +43,6 @@ public ManagedBuildCoreTests(String name) {
 		super(name);
 	}
 
-	public static Test suite() {
-		TestSuite suite = new TestSuite(ManagedBuildCoreTests.class.getName());
-		suite.addTest(new ManagedBuildCoreTests("testLoadManifest"));
-		suite.addTest(new ManagedBuildCoreTests("testTreeOptions"));
-		suite.addTest(new ManagedBuildCoreTests("testOptionsAttributeUseByScannerDiscovery"));
-		return suite;
-	}
-
 	/**
 	 * Navigates through a CDT 2.1 manifest file and verifies that the
 	 * definitions are loaded correctly.
@@ -673,4 +662,19 @@ public void testOptionsAttributeUseByScannerDiscovery() throws Exception {
 		assertNotNull(option);
 		assertEquals(true, option.isForScannerDiscovery());
 	}
+
+	/**
+	 * Tests attribute excludedFromScannerDiscovery.
+	 * @throws Exception
+	 */
+	public void testExcludedFromScannerDiscovery() throws Exception {
+		IOption optionNotExcludedFromSD = ManagedBuildManager
+				.getExtensionOption("cdt.managedbuilder.lsp.tests.option.not-excluded-sd");
+		assertNotNull(optionNotExcludedFromSD);
+		assertEquals(false, optionNotExcludedFromSD.isExcludedFromScannerDiscovery());
+
+		IOption option = ManagedBuildManager.getExtensionOption("cdt.managedbuilder.lsp.tests.option.is-excluded-sd");
+		assertNotNull(option);
+		assertEquals(true, option.isExcludedFromScannerDiscovery());
+	}
 } // end class
diff --git a/build/org.eclipse.cdt.managedbuilder.core/plugin.xml b/build/org.eclipse.cdt.managedbuilder.core/plugin.xml
index f4892de8a22..e9a85e6f67e 100644
--- a/build/org.eclipse.cdt.managedbuilder.core/plugin.xml
+++ b/build/org.eclipse.cdt.managedbuilder.core/plugin.xml
@@ -602,7 +602,7 @@
             class="org.eclipse.cdt.managedbuilder.language.settings.providers.GCCBuiltinSpecsDetector"
             id="org.eclipse.cdt.managedbuilder.core.GCCBuiltinSpecsDetector"
             name="%GCCBuiltinCompilerSettings.name"
-            parameter="${COMMAND} ${FLAGS} -E -P -v -dD &quot;${INPUTS}&quot;"
+            parameter="${COMMAND} ${ALL_FLAGS} -E -P -v -dD &quot;${INPUTS}&quot;"
             prefer-non-shared="true">
          <language-scope id="org.eclipse.cdt.core.gcc"/>
          <language-scope id="org.eclipse.cdt.core.g++"/>
@@ -611,7 +611,7 @@
             class="org.eclipse.cdt.managedbuilder.internal.language.settings.providers.GCCBuiltinSpecsDetectorCygwin"
             id="org.eclipse.cdt.managedbuilder.core.GCCBuiltinSpecsDetectorCygwin"
             name="%GCCBuiltinCompilerSettingsCygwin.name"
-            parameter="${COMMAND} ${FLAGS} -E -P -v -dD &quot;${INPUTS}&quot;"
+            parameter="${COMMAND} ${ALL_FLAGS} -E -P -v -dD &quot;${INPUTS}&quot;"
             prefer-non-shared="true">
          <language-scope id="org.eclipse.cdt.core.gcc"/>
          <language-scope id="org.eclipse.cdt.core.g++"/>
@@ -620,7 +620,7 @@
             class="org.eclipse.cdt.managedbuilder.internal.language.settings.providers.GCCBuiltinSpecsDetectorMinGW"
             id="org.eclipse.cdt.managedbuilder.core.GCCBuiltinSpecsDetectorMinGW"
             name="%GCCBuiltinCompilerSettingsMinGW.name"
-            parameter="${COMMAND} ${FLAGS} -E -P -v -dD &quot;${INPUTS}&quot;"
+            parameter="${COMMAND} ${ALL_FLAGS} -E -P -v -dD &quot;${INPUTS}&quot;"
             prefer-non-shared="true">
          <language-scope id="org.eclipse.cdt.core.gcc"/>
          <language-scope id="org.eclipse.cdt.core.g++"/>
diff --git a/build/org.eclipse.cdt.managedbuilder.core/schema/buildDefinitions.exsd b/build/org.eclipse.cdt.managedbuilder.core/schema/buildDefinitions.exsd
index f67abbe3f01..5fe85c290cb 100644
--- a/build/org.eclipse.cdt.managedbuilder.core/schema/buildDefinitions.exsd
+++ b/build/org.eclipse.cdt.managedbuilder.core/schema/buildDefinitions.exsd
@@ -707,7 +707,7 @@ The pathConverter of a toolchain applies for all tools of the toolchain except i
          <attribute name="commandLinePattern" type="string">
             <annotation>
                <documentation>
-                  Specifies the command &quot;pattern&quot; that indicates how the parts of the command line are used to create the entire command line.  The pattern consists of the replaceable variables COMMAND, FLAGS, OUTPUT_FLAG, OUTPUT_PREFIX, OUTPUT and INPUTS.  The default command line pattern is ${COMMAND} ${FLAGS} ${OUTPUT_FLAG}${OUTPUT_PREFIX}${OUTPUT} ${INPUTS}, except when customBuildStep is true, where the default is $(COMMAND). White space and other characters are significant and are copied to the generated command.  This attribute supports MBS file context macros.
+                  Specifies the command &quot;pattern&quot; that indicates how the parts of the command line are used to create the entire command line.  The pattern consists of the replaceable variables COMMAND, FLAGS, OUTPUT_FLAG, OUTPUT_PREFIX, OUTPUT and INPUTS.  The default command line pattern is ${COMMAND} ${ALL_FLAGS} ${OUTPUT_FLAG}${OUTPUT_PREFIX}${OUTPUT} ${INPUTS}, except when customBuildStep is true, where the default is $(COMMAND). White space and other characters are significant and are copied to the generated command.  This attribute supports MBS file context macros.
                </documentation>
             </annotation>
          </attribute>
@@ -1410,7 +1410,14 @@ Additional special types exist to flag options of special relevance to the build
          <attribute name="useByScannerDiscovery" type="boolean">
             <annotation>
                <documentation>
-                  An optional field to allow the option additionally to be passed to scanner discovery of built-in compiler macros and paths. The default is false.
+                  An optional field to allow the option additionally to be passed to scanner discovery of built-in compiler macros and paths in the ${FLAGS} variable. The default is false.
+               </documentation>
+            </annotation>
+         </attribute>
+         <attribute name="excludeFromScannerDiscovery" type="boolean">
+            <annotation>
+               <documentation>
+                  An optional field to allow the option to be excluded from scanner discovery's ${ALL_FLAGS} variable. The default is false.
                </documentation>
             </annotation>
          </attribute>
diff --git a/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/core/IOption.java b/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/core/IOption.java
index d296ff09c0d..f77a5f73bc1 100644
--- a/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/core/IOption.java
+++ b/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/core/IOption.java
@@ -106,6 +106,8 @@ public interface IOption extends IBuildObject {
 	public static final String COMMAND_FALSE = "commandFalse"; //$NON-NLS-1$
 	/** @since 8.3 */
 	public static final String USE_BY_SCANNER_DISCOVERY = "useByScannerDiscovery"; //$NON-NLS-1$
+	/** @since 9.5 */
+	public static final String EXCLUDE_FROM_SCANNER_DISCOVERY = "excludeFromScannerDiscovery"; //$NON-NLS-1$
 	/** @since 8.0 */
 	public static final String COMMAND_GENERATOR = "commandGenerator"; //$NON-NLS-1$
 	public static final String TOOL_TIP = "tip"; //$NON-NLS-1$
@@ -630,6 +632,15 @@ public interface IOption extends IBuildObject {
 	 */
 	public boolean isForScannerDiscovery();
 
+	/**
+	 * Flag to indicate whether the option should be excluded from scanner discovery.
+	 * @return {@code true} if the option should never be passed to scanner discovery command
+	 *    or {@code false} otherwise.
+	 *
+	 * @since 9.5
+	 */
+	public boolean isExcludedFromScannerDiscovery();
+
 	/**
 	 * Returns the tree root of this option if it is of type {@link #TREE}
 	 * @return tree root of this option or <code>null</code> if not found.
diff --git a/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/core/Option.java b/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/core/Option.java
index 393df9fe958..8671c29c25e 100644
--- a/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/core/Option.java
+++ b/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/core/Option.java
@@ -81,6 +81,7 @@ public class Option extends BuildObject implements IOption, IBuildPropertiesRest
 	private IOptionCommandGenerator commandGenerator;
 	private String commandFalse;
 	private Boolean isForScannerDiscovery;
+	private Boolean isExcludedFromScannerDiscovery;
 	private String tip;
 	private String contextId;
 	private List<String> applicableValuesList;
@@ -224,6 +225,9 @@ public Option(IHoldsOptions parent, String Id, String name, Option option) {
 		if (option.isForScannerDiscovery != null) {
 			isForScannerDiscovery = option.isForScannerDiscovery;
 		}
+		if (option.isExcludedFromScannerDiscovery != null) {
+			isExcludedFromScannerDiscovery = option.isExcludedFromScannerDiscovery;
+		}
 		if (option.tip != null) {
 			tip = option.tip;
 		}
@@ -405,6 +409,12 @@ protected void loadFromManifest(IManagedConfigElement element) {
 			isForScannerDiscovery = Boolean.parseBoolean(isForSD);
 		}
 
+		// isNotForScannerDiscovery
+		String isExcludeFromSD = element.getAttribute(EXCLUDE_FROM_SCANNER_DISCOVERY);
+		if (isExcludeFromSD != null) {
+			isExcludedFromScannerDiscovery = Boolean.parseBoolean(isExcludeFromSD);
+		}
+
 		// Get the tooltip for the option
 		tip = SafeStringInterner.safeIntern(element.getAttribute(TOOL_TIP));
 
@@ -578,6 +588,14 @@ protected void loadFromProject(ICStorageElement element) {
 			}
 		}
 
+		// isNotForScannerDiscovery
+		if (element.getAttribute(EXCLUDE_FROM_SCANNER_DISCOVERY) != null) {
+			String isExcludeFromSD = element.getAttribute(EXCLUDE_FROM_SCANNER_DISCOVERY);
+			if (isExcludeFromSD != null) {
+				isForScannerDiscovery = Boolean.parseBoolean(isExcludeFromSD);
+			}
+		}
+
 		// Get the tooltip for the option
 		if (element.getAttribute(TOOL_TIP) != null) {
 			tip = SafeStringInterner.safeIntern(element.getAttribute(TOOL_TIP));
@@ -887,6 +905,10 @@ public void serialize(ICStorageElement element) throws BuildException {
 			element.setAttribute(USE_BY_SCANNER_DISCOVERY, isForScannerDiscovery.toString());
 		}
 
+		if (isExcludedFromScannerDiscovery != null) {
+			element.setAttribute(EXCLUDE_FROM_SCANNER_DISCOVERY, isExcludedFromScannerDiscovery.toString());
+		}
+
 		if (tip != null) {
 			element.setAttribute(TOOL_TIP, tip);
 		}
@@ -1381,6 +1403,14 @@ public boolean isForScannerDiscovery() {
 		return isForScannerDiscovery;
 	}
 
+	@Override
+	public boolean isExcludedFromScannerDiscovery() {
+		if (isExcludedFromScannerDiscovery == null) {
+			isExcludedFromScannerDiscovery = superClass != null && superClass.isExcludedFromScannerDiscovery();
+		}
+		return isExcludedFromScannerDiscovery;
+	}
+
 	@Override
 	public String getToolTip() {
 		if (tip == null) {
diff --git a/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/core/OptionReference.java b/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/core/OptionReference.java
index f1bdb6a3732..5769d596956 100644
--- a/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/core/OptionReference.java
+++ b/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/core/OptionReference.java
@@ -926,6 +926,11 @@ public boolean isForScannerDiscovery() {
 		return option.isForScannerDiscovery();
 	}
 
+	@Override
+	public boolean isExcludedFromScannerDiscovery() {
+		return option.isExcludedFromScannerDiscovery();
+	}
+
 	@Override
 	public ITreeRoot getTreeRoot() {
 		if (!resolved) {
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 9b01d256fa6..a8888d5bb0f 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
@@ -105,7 +105,7 @@
 public class Tool extends HoldsOptions
 		implements ITool, IOptionCategory, IMatchKeyProvider<Tool>, IRealBuildObjectAssociation {
 
-	public static final String DEFAULT_PATTERN = "${COMMAND} ${FLAGS} ${OUTPUT_FLAG} ${OUTPUT_PREFIX}${OUTPUT} ${INPUTS} ${EXTRA_FLAGS}"; //$NON-NLS-1$
+	public static final String DEFAULT_PATTERN = "${COMMAND} ${ALL_FLAGS} ${OUTPUT_FLAG} ${OUTPUT_PREFIX}${OUTPUT} ${INPUTS} ${EXTRA_FLAGS}"; //$NON-NLS-1$
 	public static final String DEFAULT_CBS_PATTERN = "${COMMAND}"; //$NON-NLS-1$
 
 	//property name for holding the rebuild state
diff --git a/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/language/settings/providers/AbstractBuiltinSpecsDetector.java b/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/language/settings/providers/AbstractBuiltinSpecsDetector.java
index 507f5c6cce7..cdac186a773 100644
--- a/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/language/settings/providers/AbstractBuiltinSpecsDetector.java
+++ b/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/language/settings/providers/AbstractBuiltinSpecsDetector.java
@@ -53,6 +53,7 @@
 import org.eclipse.cdt.internal.core.BuildRunnerHelper;
 import org.eclipse.cdt.internal.core.XmlUtil;
 import org.eclipse.cdt.internal.core.envvar.EnvironmentVariableManager;
+import org.eclipse.cdt.managedbuilder.core.IOption;
 import org.eclipse.cdt.managedbuilder.core.ManagedBuilderCorePlugin;
 import org.eclipse.cdt.managedbuilder.internal.core.ManagedMakeMessages;
 import org.eclipse.cdt.utils.CommandLineUtil;
@@ -101,6 +102,8 @@ public abstract class AbstractBuiltinSpecsDetector extends AbstractLanguageSetti
 	protected static final String COMPILER_MACRO = "${COMMAND}"; //$NON-NLS-1$
 	/** @since 8.3 */
 	protected static final String FLAGS_MACRO = "${FLAGS}"; //$NON-NLS-1$
+	/**	@since 9.5*/
+	protected static final String ALL_FLAGS_MACRO = "${ALL_FLAGS}"; //$NON-NLS-1$
 	protected static final String SPEC_FILE_MACRO = "${INPUTS}"; //$NON-NLS-1$
 	protected static final String SPEC_EXT_MACRO = "${EXT}"; //$NON-NLS-1$
 	protected static final String SPEC_FILE_BASE = "spec"; //$NON-NLS-1$
@@ -279,6 +282,7 @@ public void shutdown() {
 	 *    Normally would come from the tool-chain.<br>
 	 * <b>${INPUTS}</b> - path to spec file which will be placed in workspace area.<br>
 	 * <b>${EXT}</b> - file extension calculated from language ID.
+	 * <b>${ALL_FLAGS}</b> - all the command line flags.
 	 * </ul>
 	 * The parameter could be taken from the extension
 	 * in {@code plugin.xml} or from property file.
@@ -334,6 +338,11 @@ protected String resolveCommand(String languageId) throws CoreException {
 				if (flags != null)
 					cmd = cmd.replace(FLAGS_MACRO, flags);
 			}
+			if (cmd.contains(ALL_FLAGS_MACRO)) {
+				String flags = getAllToolOptions(languageId);
+				if (flags != null)
+					cmd = cmd.replace(ALL_FLAGS_MACRO, flags);
+			}
 			if (cmd.contains(SPEC_FILE_MACRO)) {
 				String specFileName = getSpecFile(languageId);
 				if (specFileName != null)
@@ -933,6 +942,9 @@ protected Optional<String> selectBestSpecFileExtension(List<String> extensions)
 	 * Determine additional options to pass to scanner discovery command.
 	 * These options are intended to come from the tool-chain.
 	 *
+	 * Unlike {@link #getAllToolOptions(String)} this method filters to only
+	 * return a subset of all options. See {@link IOption#isForScannerDiscovery()}
+	 *
 	 * @param languageId - language ID.
 	 * @return additional options to pass to scanner discovery command.
 	 *
@@ -942,6 +954,23 @@ protected String getToolOptions(String languageId) {
 		return ""; //$NON-NLS-1$
 	}
 
+	/**
+	 * Determine additional options to pass to scanner discovery command.
+	 * These options are intended to come from the tool-chain.
+	 *
+	 * Unlike {@link #getToolOptions(String)} this returns all options,
+	 * except for those specifically excluded from scanner discovery
+	 * with {@link IOption#isExcludedFromScannerDiscovery()}
+	 *
+	 * @param languageId - language ID.
+	 * @return additional options to pass to scanner discovery command.
+	 *
+	 * @since 9.5
+	 */
+	protected String getAllToolOptions(String languageId) {
+		return ""; //$NON-NLS-1$
+	}
+
 	@Override
 	public Element serializeAttributes(Element parentElement) {
 		Element elementProvider = super.serializeAttributes(parentElement);
diff --git a/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/language/settings/providers/ToolchainBuiltinSpecsDetector.java b/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/language/settings/providers/ToolchainBuiltinSpecsDetector.java
index 59312318f0a..7faf3910c32 100644
--- a/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/language/settings/providers/ToolchainBuiltinSpecsDetector.java
+++ b/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/language/settings/providers/ToolchainBuiltinSpecsDetector.java
@@ -21,6 +21,7 @@
 import java.util.List;
 import java.util.Map;
 import java.util.Optional;
+import java.util.function.Predicate;
 
 import org.eclipse.cdt.core.envvar.IEnvironmentVariable;
 import org.eclipse.cdt.managedbuilder.core.BuildException;
@@ -153,8 +154,10 @@ protected String getSpecFileExtension(String languageId) {
 		return extension.get();
 	}
 
-	@Override
-	protected String getToolOptions(String languageId) {
+	/**
+	 * @since 9.5
+	 */
+	protected String getToolOptions(String languageId, Predicate<IOption> predicate) {
 		Optional<IOption[]> found = languageTool(languageId).flatMap(t -> Optional.of(t.getOptions()));
 		if (!found.isPresent()) {
 			return ""; //$NON-NLS-1$
@@ -162,7 +165,7 @@ protected String getToolOptions(String languageId) {
 		StringBuilder flags = new StringBuilder();
 		IOption[] options = found.get();
 		for (IOption option : options) {
-			if (option.isForScannerDiscovery()) {
+			if (predicate.test(option)) {
 				try {
 					String optionValue = null;
 					switch (option.getBasicValueType()) {
@@ -207,6 +210,16 @@ protected String getToolOptions(String languageId) {
 		return flags.toString().trim();
 	}
 
+	@Override
+	protected String getToolOptions(String languageId) {
+		return getToolOptions(languageId, IOption::isForScannerDiscovery);
+	}
+
+	@Override
+	protected String getAllToolOptions(String languageId) {
+		return getToolOptions(languageId, Predicate.not(IOption::isExcludedFromScannerDiscovery));
+	}
+
 	@Override
 	protected List<IEnvironmentVariable> getEnvironmentVariables() {
 		if (envMngr == null && currentCfgDescription == null) {
diff --git a/build/org.eclipse.cdt.managedbuilder.gnu.ui/plugin.properties b/build/org.eclipse.cdt.managedbuilder.gnu.ui/plugin.properties
index 95a5857e601..85c8969abb0 100644
--- a/build/org.eclipse.cdt.managedbuilder.gnu.ui/plugin.properties
+++ b/build/org.eclipse.cdt.managedbuilder.gnu.ui/plugin.properties
@@ -188,6 +188,8 @@ Option.Posix.Warn.wwritestring=Treat strings always as const (-Wwrite-strings)
 
 Option.Posix.Verbose=Verbose (-v)
 Option.OtherFlags=Other flags
+Option.OtherFlagsExcludedFromScannerDiscovery=Other flags (excluded from discovery)
+Option.OtherFlagsExcludedFromScannerDiscoveryTip=Flags that will not be passed to the compiler when discovering compiler built-in macros and include paths. Include compiler flags here that may interfere with the correct operation of scanner discovery.  
 Option.Posix.Ansi=Support ANSI programs (-ansi)
 Option.PIC=Position Independent Code (-fPIC)
 Option.codecov=Generate gcov information (-ftest-coverage -fprofile-arcs)
diff --git a/build/org.eclipse.cdt.managedbuilder.gnu.ui/plugin.xml b/build/org.eclipse.cdt.managedbuilder.gnu.ui/plugin.xml
index e35e6ee04c0..345b44f4a0c 100644
--- a/build/org.eclipse.cdt.managedbuilder.gnu.ui/plugin.xml
+++ b/build/org.eclipse.cdt.managedbuilder.gnu.ui/plugin.xml
@@ -1440,6 +1440,15 @@
 			  id="gnu.c.compiler.option.misc.other"
 			  valueType="string">
 		  </option>
+		  <option
+			  defaultValue=""
+			  name="%Option.OtherFlagsExcludedFromScannerDiscovery"
+			  tip="%Option.OtherFlagsExcludedFromScannerDiscoveryTip"
+			  category="gnu.c.compiler.category.other"
+			  id="gnu.c.compiler.option.misc.otherExcludedFromScannerDiscovery"
+			  excludeFromScannerDiscovery="true"
+			  valueType="string">
+		  </option>
 		  <option
 			  defaultValue="false"
 			  name="%Option.Posix.Verbose"
@@ -2036,6 +2045,15 @@
 			  id="gnu.cpp.compiler.option.other.other"
 			  valueType="string">
 		  </option>
+		  <option
+			  defaultValue=""
+			  name="%Option.OtherFlagsExcludedFromScannerDiscovery"
+			  tip="%Option.OtherFlagsExcludedFromScannerDiscoveryTip"
+			  category="gnu.cpp.compiler.category.other"
+			  id="gnu.cpp.compiler.option.other.otherExcludedFromScannerDiscovery"
+			  excludeFromScannerDiscovery="true"
+			  valueType="string">
+		  </option>
 		  <option
 			  defaultValue="false"
 			  name="%Option.Posix.Verbose"
diff --git a/build/org.eclipse.cdt.managedbuilder.ui/src/org/eclipse/cdt/managedbuilder/ui/properties/ToolSettingsTab.java b/build/org.eclipse.cdt.managedbuilder.ui/src/org/eclipse/cdt/managedbuilder/ui/properties/ToolSettingsTab.java
index 671185fbf1e..e9a7f042bfb 100644
--- a/build/org.eclipse.cdt.managedbuilder.ui/src/org/eclipse/cdt/managedbuilder/ui/properties/ToolSettingsTab.java
+++ b/build/org.eclipse.cdt.managedbuilder.ui/src/org/eclipse/cdt/managedbuilder/ui/properties/ToolSettingsTab.java
@@ -569,7 +569,7 @@ protected void addFilter(ViewerFilter filter) {
 	 */
 	protected void setOption(IOption op1, IOption op2, IHoldsOptions dst, IResourceInfo res) {
 		try {
-			if (op1.isForScannerDiscovery() && ((Option) op1).isDirty())
+			if (((Option) op1).isDirty())
 				isIndexerAffected = true;
 			switch (op1.getValueType()) {
 			case IOption.BOOLEAN:
@@ -596,8 +596,6 @@ protected void setOption(IOption op1, IOption op2, IHoldsOptions dst, IResourceI
 			case IOption.UNDEF_LIBRARY_PATHS:
 			case IOption.UNDEF_LIBRARY_FILES:
 			case IOption.UNDEF_MACRO_FILES:
-				if (((Option) op1).isDirty())
-					isIndexerAffected = true;
 				@SuppressWarnings("unchecked")
 				String[] data = ((List<String>) op1.getValue()).toArray(new String[0]);
 				ManagedBuildManager.setOption(res, dst, op2, data);
@@ -793,28 +791,7 @@ protected void performOK() {
 			IOption op1[] = t.getOptions();
 			for (IOption op : op1) {
 				if (((Option) op).isDirty()) {
-					if (op.isForScannerDiscovery())
-						isIndexerAffected = true;
-					else {
-						try {
-							switch (op.getValueType()) {
-							case IOption.INCLUDE_PATH:
-							case IOption.PREPROCESSOR_SYMBOLS:
-							case IOption.INCLUDE_FILES:
-							case IOption.MACRO_FILES:
-							case IOption.UNDEF_INCLUDE_PATH:
-							case IOption.UNDEF_PREPROCESSOR_SYMBOLS:
-							case IOption.UNDEF_INCLUDE_FILES:
-							case IOption.UNDEF_LIBRARY_PATHS:
-							case IOption.UNDEF_LIBRARY_FILES:
-							case IOption.UNDEF_MACRO_FILES:
-								isIndexerAffected = true;
-								break;
-							}
-						} catch (BuildException e) {
-							// Do nothing
-						}
-					}
+					isIndexerAffected = true;
 				}
 			}
 		}
diff --git a/core/org.eclipse.cdt.ui/src/org/eclipse/cdt/internal/ui/newui/Messages.java b/core/org.eclipse.cdt.ui/src/org/eclipse/cdt/internal/ui/newui/Messages.java
index df64bb6c6e3..d1ead212835 100644
--- a/core/org.eclipse.cdt.ui/src/org/eclipse/cdt/internal/ui/newui/Messages.java
+++ b/core/org.eclipse.cdt.ui/src/org/eclipse/cdt/internal/ui/newui/Messages.java
@@ -54,6 +54,7 @@ public class Messages extends NLS {
 	public static String AbstractPage_7;
 	public static String AbstractPage_8;
 	public static String AbstractPage_9;
+	public static String AbstractPage_Rebuild_Index;
 	public static String AbstractPage_rebuildIndex_question;
 	public static String BinaryParsTab_0;
 	public static String BrowseEntryDialog_dir_title_add;
diff --git a/core/org.eclipse.cdt.ui/src/org/eclipse/cdt/internal/ui/newui/Messages.properties b/core/org.eclipse.cdt.ui/src/org/eclipse/cdt/internal/ui/newui/Messages.properties
index 3c6bb620d97..1c126d1be7a 100644
--- a/core/org.eclipse.cdt.ui/src/org/eclipse/cdt/internal/ui/newui/Messages.properties
+++ b/core/org.eclipse.cdt.ui/src/org/eclipse/cdt/internal/ui/newui/Messages.properties
@@ -101,7 +101,8 @@ AbstractPage_6=Configuration:\u0020
 AbstractPage_7=Exclude resource from build
 AbstractPage_8=Cannot apply
 AbstractPage_9=Internal error
-AbstractPage_rebuildIndex_question=Changes made will not be reflected in the index until it is rebuilt. Do you wish to rebuild it now?
+AbstractPage_Rebuild_Index=Rebuild Index
+AbstractPage_rebuildIndex_question=Some build settings changes may affect the index. These changes won't take effect until the index until it is rebuilt. Do you wish to rebuild it now?
 
 AbstractLangsListTab_ShowBuiltin=Show built-in values
 AbstractLangsListTab_Languages=Languages
diff --git a/core/org.eclipse.cdt.ui/src/org/eclipse/cdt/ui/newui/AbstractPage.java b/core/org.eclipse.cdt.ui/src/org/eclipse/cdt/ui/newui/AbstractPage.java
index a1a74109872..7e8ed167dcd 100644
--- a/core/org.eclipse.cdt.ui/src/org/eclipse/cdt/ui/newui/AbstractPage.java
+++ b/core/org.eclipse.cdt.ui/src/org/eclipse/cdt/ui/newui/AbstractPage.java
@@ -751,7 +751,8 @@ private void rebuildIndex() {
 		final String title = getTitle();
 		final String msg = Messages.AbstractPage_rebuildIndex_question;
 		int result = OptionalMessageDialog.open(PREF_ASK_REINDEX, shell, title, null /* default image */, msg,
-				MessageDialog.QUESTION, new String[] { IDialogConstants.YES_LABEL, IDialogConstants.NO_LABEL }, 0);
+				MessageDialog.QUESTION, new String[] { Messages.AbstractPage_Rebuild_Index, IDialogConstants.NO_LABEL },
+				0);
 		if (result == OptionalMessageDialog.NOT_SHOWN) {
 			result = OptionalMessageDialog.getDialogDetail(PREF_ASK_REINDEX);
 		} else if (result != SWT.DEFAULT) {
diff --git a/cross/org.eclipse.cdt.build.crossgcc/plugin.xml b/cross/org.eclipse.cdt.build.crossgcc/plugin.xml
index d7f5eca6409..c1b29fe0e4d 100644
--- a/cross/org.eclipse.cdt.build.crossgcc/plugin.xml
+++ b/cross/org.eclipse.cdt.build.crossgcc/plugin.xml
@@ -267,7 +267,7 @@
             class="org.eclipse.cdt.internal.build.crossgcc.CrossGCCBuiltinSpecsDetector"
             id="org.eclipse.cdt.build.crossgcc.CrossGCCBuiltinSpecsDetector"
             name="%CrossGCCBuiltinSpecsDetector.name"
-            parameter="${COMMAND} ${FLAGS} -E -P -v -dD &quot;${INPUTS}&quot;"
+            parameter="${COMMAND} ${ALL_FLAGS} -E -P -v -dD &quot;${INPUTS}&quot;"
             prefer-non-shared="true">
          <language-scope id="org.eclipse.cdt.core.gcc"/>
          <language-scope id="org.eclipse.cdt.core.g++"/>
diff --git a/debug/org.eclipse.cdt.debug.application.doc/reference/cdt_u_pref_build_scanner_discovery.htm b/debug/org.eclipse.cdt.debug.application.doc/reference/cdt_u_pref_build_scanner_discovery.htm
index 33baf04b006..076214d57f7 100644
--- a/debug/org.eclipse.cdt.debug.application.doc/reference/cdt_u_pref_build_scanner_discovery.htm
+++ b/debug/org.eclipse.cdt.debug.application.doc/reference/cdt_u_pref_build_scanner_discovery.htm
@@ -183,6 +183,8 @@ <h3>Builtin Compiler Settings Provider Options</h3>
 				<ul>
 					<li><strong>${COMMAND}</strong> - compiler command from the tool-chain, such as "gcc".</li>
 					<li><strong>${FLAGS}</strong> - applicable compiler flags from the tool-chain, such as language dialect flag "-std=c++0x".</li>
+					<li><strong>${ALL_FLAGS}</strong> - all compiler flags from the tool-chain, except those explicity excluded, 
+						either by tool provider or by being entered in the "Other flags (excluded from discovery)" in the "Miscellaneous" tool page. </li>
 					<li><strong>${INPUTS}</strong> - indicates normally an empty specs file required by the compiler.
 						If no such file exists the file gets created temporarily in Eclipse workspace plugin area.
 					</li>
diff --git a/doc/org.eclipse.cdt.doc.user/reference/cdt_u_pref_build_scanner_discovery.htm b/doc/org.eclipse.cdt.doc.user/reference/cdt_u_pref_build_scanner_discovery.htm
index 33baf04b006..076214d57f7 100644
--- a/doc/org.eclipse.cdt.doc.user/reference/cdt_u_pref_build_scanner_discovery.htm
+++ b/doc/org.eclipse.cdt.doc.user/reference/cdt_u_pref_build_scanner_discovery.htm
@@ -183,6 +183,8 @@ <h3>Builtin Compiler Settings Provider Options</h3>
 				<ul>
 					<li><strong>${COMMAND}</strong> - compiler command from the tool-chain, such as "gcc".</li>
 					<li><strong>${FLAGS}</strong> - applicable compiler flags from the tool-chain, such as language dialect flag "-std=c++0x".</li>
+					<li><strong>${ALL_FLAGS}</strong> - all compiler flags from the tool-chain, except those explicity excluded, 
+						either by tool provider or by being entered in the "Other flags (excluded from discovery)" in the "Miscellaneous" tool page. </li>
 					<li><strong>${INPUTS}</strong> - indicates normally an empty specs file required by the compiler.
 						If no such file exists the file gets created temporarily in Eclipse workspace plugin area.
 					</li>
diff --git a/windows/org.eclipse.cdt.msw.build/plugin.xml b/windows/org.eclipse.cdt.msw.build/plugin.xml
index c8e8d75b575..1a1198d4fa1 100644
--- a/windows/org.eclipse.cdt.msw.build/plugin.xml
+++ b/windows/org.eclipse.cdt.msw.build/plugin.xml
@@ -768,7 +768,7 @@
             class="org.eclipse.cdt.internal.msw.build.core.ClangClBuiltinSpecsDetector"
             id="org.eclipse.cdt.msw.build.core.ClangCLBuiltinSpecsDetector"
             name="%ClangCLBuiltinSpecsDetector.name"
-            parameter="${COMMAND} ${FLAGS} -E /clang:-P -v /clang:-dD &quot;${INPUTS}&quot;"
+            parameter="${COMMAND} ${ALL_FLAGS} -E /clang:-P -v /clang:-dD &quot;${INPUTS}&quot;"
             prefer-non-shared="true">
          <language-scope id="org.eclipse.cdt.core.gcc"/>
          <language-scope id="org.eclipse.cdt.core.g++"/>