diff --git a/build/org.eclipse.cdt.autotools.core/plugin.properties b/build/org.eclipse.cdt.autotools.core/plugin.properties
index 19c5089a1a5..152345d54af 100644
--- a/build/org.eclipse.cdt.autotools.core/plugin.properties
+++ b/build/org.eclipse.cdt.autotools.core/plugin.properties
@@ -22,6 +22,7 @@ Autotools.wizard.name=GNU Autotools Build Wizard
 Autoconf.editor.name=Autoconf Editor
 
 BuildProperty.value.name.default=Default;
+BuildProperty.value.name.debug=Debug
 BuildProperty.type.name.autotools=GNU Autotools
 
 PreferenceAutotools.name=Autotools
@@ -45,6 +46,7 @@ Autotools.projecttype.name=GNU Autotools
 AutotoolsNature.name=Autotools Project Nature
 AutotoolsNewNature.name=Autotools Project Nature V2
 Configuration.build.name=Build (GNU)
+Configuration.debug.name=Debug (GNU)
 Autotools.targetplatform.name=GNU Autotools Target Platform
 Autotools.gnu.toolchain.name=GNU Autotools Toolchain
 Configure.outputType=Configure Output (config.status)
diff --git a/build/org.eclipse.cdt.autotools.core/plugin.xml b/build/org.eclipse.cdt.autotools.core/plugin.xml
index 261d653ee3c..27493675eeb 100644
--- a/build/org.eclipse.cdt.autotools.core/plugin.xml
+++ b/build/org.eclipse.cdt.autotools.core/plugin.xml
@@ -10,6 +10,10 @@
               	property="org.eclipse.cdt.build.core.buildType" 
               	id="org.eclipse.linuxtools.cdt.autotools.core.buildType.default" 
               	name="%BuildProperty.value.name.default"/>
+           <propertyValue 
+              	property="org.eclipse.cdt.build.core.buildType" 
+              	id="org.eclipse.linuxtools.cdt.autotools.core.buildType.debug" 
+              	name="%BuildProperty.value.name.debug"/>
            <propertyValue 
             	property="org.eclipse.cdt.build.core.buildArtefactType" 
             	id="org.eclipse.linuxtools.cdt.autotools.core.buildArtefactType.autotools" 
@@ -332,7 +336,17 @@
                name="%Option.configure.user"
                resourceFilter="all"
                tip="%Option.configure.user.tip"
-               valueType="string"/>
+               valueType="string">
+               <enablement
+              		type="CONTAINER_ATTRIBUTE" 
+              		attribute="defaultValue" 
+              		value="CFLAGS=-g -O0"
+              		extensionAdjustment="false">
+			  		<checkBuildProperty 
+			  			property="org.eclipse.cdt.build.core.buildType"
+			  			value="org.eclipse.linuxtools.cdt.autotools.core.buildType.debug"/>
+               </enablement>
+         </option>
          <outputType
                id="org.eclipse.linuxtools.cdt.autotools.core.outputType.configure"
                name="%Configure.outputType"
@@ -388,7 +402,7 @@
             id="org.eclipse.linuxtools.cdt.autotools.core.projectType"
             isAbstract="false">
          <configuration
-               buildProperties="org.eclipse.linuxtools.cdt.autotools.core.buildType.default"
+               buildProperties="org.eclipse.cdt.build.core.buildType=org.eclipse.linuxtools.cdt.autotools.core.buildType.default"
                cleanCommand="rm -rf"
                errorParsers="org.eclipse.cdt.core.CWDLocator;org.eclipse.cdt.core.GmakeErrorParser;org.eclipse.cdt.core.GCCErrorParser;org.eclipse.cdt.core.GLDErrorParser;org.eclipse.cdt.core.GASErrorParser"
                id="org.eclipse.linuxtools.cdt.autotools.core.configuration.build"
@@ -432,6 +446,65 @@
                <builder
                      id="org.eclipse.linuxtools.cdt.autotools.core.toolchain.builder"
                      isAbstract="false"
+                     isVariableCaseSensitive="false"
+                     name="%Makefile.builder.name">
+               </builder>
+               <supportedProperties>
+                  <property
+                        id="org.eclipse.cdt.build.core.buildArtefactType">
+                     <value
+                           id="org.eclipse.linuxtools.cdt.autotools.core.buildArtefactType.autotools">
+                     </value>
+                  </property>
+               </supportedProperties>
+            </toolChain>
+         </configuration>
+          <configuration
+               buildProperties="org.eclipse.cdt.build.core.buildType=org.eclipse.linuxtools.cdt.autotools.core.buildType.debug"
+               cleanCommand="rm -rf"
+               errorParsers="org.eclipse.cdt.core.CWDLocator;org.eclipse.cdt.core.GmakeErrorParser;org.eclipse.cdt.core.GCCErrorParser;org.eclipse.cdt.core.GLDErrorParser;org.eclipse.cdt.core.GASErrorParser"
+               id="org.eclipse.linuxtools.cdt.autotools.core.configuration.build.debug"
+               languageSettingsProviders="org.eclipse.cdt.ui.UserLanguageSettingsProvider;org.eclipse.cdt.core.ReferencedProjectsLanguageSettingsProvider;org.eclipse.cdt.managedbuilder.core.MBSLanguageSettingsProvider;${Toolchain}"
+               name="%Configuration.debug.name">
+            <toolChain
+                  archList="all"
+                  configurationEnvironmentSupplier="org.eclipse.cdt.internal.autotools.core.AutotoolsEnvironmentVariableSupplier"
+                  id="org.eclipse.linuxtools.cdt.autotools.core.toolChain.debug"
+                  languageSettingsProviders="org.eclipse.cdt.autotools.core.LibtoolGCCBuildCommandParser;org.eclipse.cdt.managedbuilder.core.GCCBuiltinSpecsDetector"
+                  name="%Autotools.gnu.toolchain.name"
+                  supportsManagedBuild="false"
+                  targetTool="org.eclipse.linuxtools.cdt.autotools.core.tool.configure">
+               <tool
+                     id="org.eclipse.linuxtools.cdt.autotools.core.gnu.toolchain.tool.configure.debug"
+                     isAbstract="false"
+                     natureFilter="both"
+                     superClass="org.eclipse.linuxtools.cdt.autotools.core.tool.configure"/>
+               <tool
+                     id="org.eclipse.linuxtools.cdt.autotools.core.toolchain.tool.autogen.debug"
+                     isAbstract="false"
+                     natureFilter="both"
+                     superClass="org.eclipse.linuxtools.cdt.autotools.core.tool.autogen">
+               </tool>
+               <tool
+                     id="org.eclipse.linuxtools.cdt.autotools.core.toolchain.tool.gcc.debug"
+                     isAbstract="false"
+                     superClass="cdt.managedbuild.tool.gnu.c.compiler">
+               </tool>
+               <tool
+                     id="org.eclipse.linuxtools.cdt.autotools.core.toolchain.tool.gpp.debug"
+                     isAbstract="false"
+                     superClass="cdt.managedbuild.tool.gnu.cpp.compiler">
+               </tool>
+               <targetPlatform
+                     id="org.eclipse.linuxtools.cdt.autotools.core.toolchain.targetPlatform.debug"
+                     isAbstract="false"
+                     name="%Autotools.targetplatform.name"
+                     superClass="org.eclipse.linuxtools.cdt.autotools.core.targetPlatform">
+               </targetPlatform>
+               <builder
+                     id="org.eclipse.linuxtools.cdt.autotools.core.toolchain.builder.debug"
+                     superClass="org.eclipse.linuxtools.cdt.autotools.core.toolchain.builder"
+                     isAbstract="false"
                      isVariableCaseSensitive="false">
                </builder>
                <supportedProperties>
@@ -441,6 +514,12 @@
                            id="org.eclipse.linuxtools.cdt.autotools.core.buildArtefactType.autotools">
                      </value>
                   </property>
+                  <property
+                        id="org.eclipse.cdt.build.core.buildType">
+                     <value
+                           id="org.eclipse.linuxtools.cdt.autotools.core.buildType.debug">
+                     </value>
+                  </property>
                </supportedProperties>
             </toolChain>
          </configuration>
diff --git a/build/org.eclipse.cdt.autotools.core/src/org/eclipse/cdt/internal/autotools/core/configure/AutotoolsConfiguration.java b/build/org.eclipse.cdt.autotools.core/src/org/eclipse/cdt/internal/autotools/core/configure/AutotoolsConfiguration.java
index 9e26fb89a80..a9a71b43681 100644
--- a/build/org.eclipse.cdt.autotools.core/src/org/eclipse/cdt/internal/autotools/core/configure/AutotoolsConfiguration.java
+++ b/build/org.eclipse.cdt.autotools.core/src/org/eclipse/cdt/internal/autotools/core/configure/AutotoolsConfiguration.java
@@ -18,6 +18,14 @@ import java.util.List;
 import java.util.Map;
 
 import org.eclipse.cdt.autotools.core.AutotoolsOptionConstants;
+import org.eclipse.cdt.core.CCProjectNature;
+import org.eclipse.cdt.core.model.CoreModel;
+import org.eclipse.cdt.core.settings.model.ICConfigurationDescription;
+import org.eclipse.cdt.managedbuilder.core.IBuildObjectProperties;
+import org.eclipse.cdt.managedbuilder.core.IConfiguration;
+import org.eclipse.cdt.managedbuilder.core.ManagedBuildManager;
+import org.eclipse.core.resources.IProject;
+import org.eclipse.core.runtime.CoreException;
 
 
 public class AutotoolsConfiguration implements IAConfiguration {
@@ -25,6 +33,7 @@ public class AutotoolsConfiguration implements IAConfiguration {
 	public static class Option {
 		private String name;
 		private String transformedName;
+		private String superClassId;
 		private int type;
 		private String defaultValue;
 		
@@ -45,6 +54,14 @@ public class AutotoolsConfiguration implements IAConfiguration {
 			this.defaultValue = defaultValue;
 		}
 		
+		public Option(String name, String transformedName, String defaultValue, String superClassId, int type) {
+			this.name = name;
+			this.transformedName = transformedName;
+			this.type = type;
+			this.defaultValue = defaultValue;
+			this.superClassId = superClassId;
+		}
+
 		public String getName() {
 			return name;
 		}
@@ -57,6 +74,10 @@ public class AutotoolsConfiguration implements IAConfiguration {
 			return defaultValue;
 		}
 		
+		public String getSuperClassId() {
+			return superClassId;
+		}
+
 		public String getDescription() {
 			return ConfigureMessages.getConfigureDescription(transformedName);
 		}
@@ -121,15 +142,21 @@ public class AutotoolsConfiguration implements IAConfiguration {
 	private String id;
 	private boolean isDirty;
 	private boolean isParmsDirty;
+	private IProject project;
 	private Map<String, IConfigureOption> configOptions;
 	private ArrayList<String> configParms = new ArrayList<>();
 
 	public AutotoolsConfiguration(String name) {
-		this(name, true);
+		this(null, name, true);
+	}
+
+	public AutotoolsConfiguration(IProject project, String name) {
+		this(project, name, true);
 	}
 		
-	private AutotoolsConfiguration(String name, boolean initialize) {
+	private AutotoolsConfiguration(IProject project, String name, boolean initialize) {
 		this.id = name;
+		this.project = project;
 		configOptions = new HashMap<>();
 		if (initialize)
 			initConfigOptions();
@@ -140,6 +167,16 @@ public class AutotoolsConfiguration implements IAConfiguration {
 		// Put configure options in hash map.  Ignore categories.
 		ArrayList<Option> tools = new ArrayList<>();
 		FlagConfigureOption lastFlag = null;
+		IConfiguration configuration = null;
+		IBuildObjectProperties buildProperties = null;
+		if (project != null) {
+			ICConfigurationDescription cfgd = CoreModel.getDefault().getProjectDescription(project)
+					.getConfigurationById(id);
+
+			configuration = ManagedBuildManager.getConfigurationForDescription(cfgd);
+			if (configuration != null)
+				buildProperties = configuration.getBuildProperties();
+		}
 		for (int i = 0; i < configOpts.length; ++i) {
 			Option opt = configOpts[i];
 			String defaultValue = opt.getDefaultValue();
@@ -165,6 +202,23 @@ public class AutotoolsConfiguration implements IAConfiguration {
 				break;
 			case IConfigureOption.MULTIARG:
 				MultiArgConfigureOption m = new MultiArgConfigureOption(opt.name, opt.transformedName, this);
+				if (buildProperties != null) {
+					// Check to see if we have a Debug configuration in which
+					// case, default the compiler flags
+					// appropriately (for C or C/C++).
+					if (opt.name.equals("user")) { //$NON-NLS-1$
+						if (buildProperties.containsValue("org.eclipse.cdt.build.core.buildType", //$NON-NLS-1$
+								"org.eclipse.linuxtools.cdt.autotools.core.buildType.debug")) { //$NON-NLS-1$
+							defaultValue = "CFLAGS='-g -O0'"; //$NON-NLS-1$
+							try {
+							if (project.hasNature(CCProjectNature.CC_NATURE_ID))
+								defaultValue += " CXXFLAGS='-g -O0'"; //$NON-NLS-1$
+							} catch (CoreException e) {
+								// do nothing
+							}
+						}
+					}
+				}
 				if (defaultValue != null)
 					m.setValue(defaultValue);
 				configOptions.put(opt.name, m);
@@ -251,12 +305,12 @@ public class AutotoolsConfiguration implements IAConfiguration {
 
 	@Override
 	public IAConfiguration copy() {
-		return copy(id);
+		return copy(this.id);
 	}
 	
 	@Override
 	public IAConfiguration copy(String newId) {
-		AutotoolsConfiguration cfg = new AutotoolsConfiguration(newId, false);
+		AutotoolsConfiguration cfg = new AutotoolsConfiguration(project, newId, false);
 		Collection<IConfigureOption> oldValues = configOptions.values();
 		for (Iterator<IConfigureOption> i = oldValues.iterator(); i.hasNext();) {
 			IConfigureOption opt = i.next();
diff --git a/build/org.eclipse.cdt.autotools.core/src/org/eclipse/cdt/internal/autotools/core/configure/AutotoolsConfigurationManager.java b/build/org.eclipse.cdt.autotools.core/src/org/eclipse/cdt/internal/autotools/core/configure/AutotoolsConfigurationManager.java
index fc1428746b5..c63fce0a565 100644
--- a/build/org.eclipse.cdt.autotools.core/src/org/eclipse/cdt/internal/autotools/core/configure/AutotoolsConfigurationManager.java
+++ b/build/org.eclipse.cdt.autotools.core/src/org/eclipse/cdt/internal/autotools/core/configure/AutotoolsConfigurationManager.java
@@ -100,6 +100,10 @@ public class AutotoolsConfigurationManager implements IResourceChangeListener {
 		return new AutotoolsConfiguration(id);
 	}
 	
+	public synchronized IAConfiguration createDefaultConfiguration(IProject project, String id) {
+		return new AutotoolsConfiguration(project, id);
+	}
+
 	public synchronized IAConfiguration findCfg(IProject p, String id) {
 		Map<String, IAConfiguration> cfgs = getConfigurations(p);
 		return cfgs.get(id);
@@ -112,7 +116,7 @@ public class AutotoolsConfigurationManager implements IResourceChangeListener {
 	public synchronized IAConfiguration getConfiguration(IProject p, String cfgId, boolean persist) {
 		IAConfiguration cfg = findCfg(p, cfgId);
 		if (cfg == null) {
-			cfg = createDefaultConfiguration(cfgId);
+			cfg = createDefaultConfiguration(p, cfgId);
 			if (persist) {
 				addConfiguration(p, cfg);
 			}
@@ -223,7 +227,7 @@ public class AutotoolsConfigurationManager implements IResourceChangeListener {
 							else
 								continue; // have to punt, this doesn't map to real cfg
 						}
-						IAConfiguration cfg = new AutotoolsConfiguration(cfgId);
+						IAConfiguration cfg = new AutotoolsConfiguration(project, cfgId);
 						NodeList l = n.getChildNodes();
 						for (int y = 0; y < l.getLength(); ++y) {
 							Node child = l.item(y);
@@ -304,7 +308,7 @@ public class AutotoolsConfigurationManager implements IResourceChangeListener {
 		if (savedList != null)
 			oldCfg = savedList.get(oldId);
 		if (oldCfg != null) {
-			IAConfiguration newCfg = oldCfg.copy(cfgd.getId());
+			IAConfiguration newCfg = oldCfg.copy(newId);
 			tmpList.put(cfgd.getId(), newCfg);
 			// Check to see if the new configuration is already stored as part of the project description.
 			// If yes, it should already be saved.  This can occur if the configuration was added as part of
@@ -394,7 +398,7 @@ public class AutotoolsConfigurationManager implements IResourceChangeListener {
 						String id = cfgd.getId();
 						IAConfiguration cfg = cfgs.get(id);
 						if (cfg == null) {
-							cfg = createDefaultConfiguration(id);
+							cfg = createDefaultConfiguration(project, id);
 						}
 						p.println("<configuration id=\"" + cfg.getId() + "\">"); //$NON-NLS-1$ //$NON-NLS-2$
 						for (int j = 0; j < optionList.length; ++j) {
@@ -626,7 +630,7 @@ public class AutotoolsConfigurationManager implements IResourceChangeListener {
 
 		// Get set of configuration options and convert to set of IAutotoolOptions
 		Map<String, IConfigureOption> cfgOptions = cfg.getOptions();
-		IAConfiguration dummyCfg = createDefaultConfiguration(createDummyId());
+		IAConfiguration dummyCfg = createDefaultConfiguration(project, createDummyId());
 		for (Iterator<Entry<String, IConfigureOption>> i = cfgOptions.entrySet().iterator(); i.hasNext();) {
 			Map.Entry<String, IConfigureOption> entry = i.next();
 			String name = entry.getKey();
diff --git a/build/org.eclipse.cdt.autotools.ui.tests/src/org/eclipse/cdt/autotools/ui/tests/SetConfigurationParameter.java b/build/org.eclipse.cdt.autotools.ui.tests/src/org/eclipse/cdt/autotools/ui/tests/SetConfigurationParameter.java
index 4720625aea1..a7bce04f3d2 100644
--- a/build/org.eclipse.cdt.autotools.ui.tests/src/org/eclipse/cdt/autotools/ui/tests/SetConfigurationParameter.java
+++ b/build/org.eclipse.cdt.autotools.ui.tests/src/org/eclipse/cdt/autotools/ui/tests/SetConfigurationParameter.java
@@ -332,7 +332,7 @@ public class SetConfigurationParameter extends AbstractTest {
 		Element e = d.getDocumentElement();
 		// Get the stored configuration data
 		NodeList cfgs = e.getElementsByTagName("configuration"); //$NON-NLS-1$
-		assertEquals(3, cfgs.getLength());
+		assertEquals(4, cfgs.getLength());
 		int foundUser = 0;
 		for (int x = 0; x < cfgs.getLength(); ++x) {
 			Node n = cfgs.item(x);