diff --git a/build/org.eclipse.cdt.build.gcc.core/src/org/eclipse/cdt/build/gcc/core/GCCToolChain.java b/build/org.eclipse.cdt.build.gcc.core/src/org/eclipse/cdt/build/gcc/core/GCCToolChain.java
index 1425a4f0da8..86af92019d3 100644
--- a/build/org.eclipse.cdt.build.gcc.core/src/org/eclipse/cdt/build/gcc/core/GCCToolChain.java
+++ b/build/org.eclipse.cdt.build.gcc.core/src/org/eclipse/cdt/build/gcc/core/GCCToolChain.java
@@ -13,6 +13,7 @@ import java.io.IOException;
 import java.io.InputStreamReader;
 import java.net.URI;
 import java.nio.file.Files;
+import java.nio.file.InvalidPathException;
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.ArrayList;
@@ -255,12 +256,12 @@ public class GCCToolChain extends PlatformObject implements IToolChain {
 			addDiscoveryOptions(commandLine);
 			commandLine.addAll(commandStrings.subList(1, commandStrings.size()));
 
-			// Strip quotes from the args on Windows
+			// Strip surrounding quotes from the args on Windows
 			if (Platform.OS_WIN32.equals(Platform.getOS())) {
 				for (int i = 0; i < commandLine.size(); i++) {
 					String arg = commandLine.get(i);
-					if (arg.contains("\"")) { //$NON-NLS-1$
-						commandLine.set(i, arg.replaceAll("\"", "")); //$NON-NLS-1$ //$NON-NLS-2$
+					if (arg.startsWith("\"") && arg.endsWith("\"")) { //$NON-NLS-1$ //$NON-NLS-2$
+						commandLine.set(i, arg.substring(1, arg.length() - 1));
 					}
 				}
 			}
@@ -284,7 +285,12 @@ public class GCCToolChain extends PlatformObject implements IToolChain {
 			for (int i = 1; i < commandLine.size(); ++i) {
 				if (!commandLine.get(i).startsWith("-")) { //$NON-NLS-1$
 					// TODO optimize by dealing with multi arg options like -o
-					Path filePath = buildDirectory.resolve(commandLine.get(i));
+					Path filePath;
+					try {
+						filePath = buildDirectory.resolve(commandLine.get(i));
+					} catch (InvalidPathException e) {
+						continue;
+					}
 					IFile[] files = ResourcesPlugin.getWorkspace().getRoot().findFilesForLocationURI(filePath.toUri());
 					if (files.length > 0 && files[0].exists()) {
 						// replace it with a temp file
@@ -479,6 +485,10 @@ public class GCCToolChain extends PlatformObject implements IToolChain {
 			} else if (cCommand.contains("clang")) { //$NON-NLS-1$
 				cppCommand = cCommand.replace("clang", "clang++"); //$NON-NLS-1$ //$NON-NLS-2$
 				commands = new String[] { cCommand, cppCommand };
+			} else if (cCommand.contains("emcc")) { //$NON-NLS-1$
+				// TODO Hack for emscripten. Can we generalize?
+				cppCommand = cCommand.replace("emcc", "em++"); //$NON-NLS-1$ //$NON-NLS-2$
+				commands = new String[] { cCommand, cppCommand };
 			} else {
 				commands = new String[] { cCommand };
 			}
diff --git a/build/org.eclipse.cdt.cmake.core/src/org/eclipse/cdt/cmake/core/internal/CMakeBuildConfiguration.java b/build/org.eclipse.cdt.cmake.core/src/org/eclipse/cdt/cmake/core/internal/CMakeBuildConfiguration.java
index 1308426d97d..14d9fae4f0b 100644
--- a/build/org.eclipse.cdt.cmake.core/src/org/eclipse/cdt/cmake/core/internal/CMakeBuildConfiguration.java
+++ b/build/org.eclipse.cdt.cmake.core/src/org/eclipse/cdt/cmake/core/internal/CMakeBuildConfiguration.java
@@ -61,12 +61,7 @@ public class CMakeBuildConfiguration extends CBuildConfiguration {
 		} else {
 			toolChainFile = manager.getToolChainFileFor(getToolChain());
 			if (toolChainFile != null) {
-				settings.put(TOOLCHAIN_FILE, toolChainFile.getPath().toString());
-				try {
-					settings.flush();
-				} catch (BackingStoreException e) {
-					Activator.log(e);
-				}
+				saveToolChainFile();
 			}
 		}
 	}
@@ -78,20 +73,20 @@ public class CMakeBuildConfiguration extends CBuildConfiguration {
 	public CMakeBuildConfiguration(IBuildConfiguration config, String name, IToolChain toolChain,
 			ICMakeToolChainFile toolChainFile, String launchMode) {
 		super(config, name, toolChain, launchMode);
-		this.toolChainFile = toolChainFile;
 
-		saveToolChainFile();
+		this.toolChainFile = toolChainFile;
+		if (toolChainFile != null) {
+			saveToolChainFile();
+		}
 	}
 
 	private void saveToolChainFile() {
-		if (toolChainFile != null) {
-			Preferences settings = getSettings();
-			settings.put(TOOLCHAIN_FILE, toolChainFile.getPath().toString());
-			try {
-				settings.flush();
-			} catch (BackingStoreException e) {
-				Activator.log(e);
-			}
+		Preferences settings = getSettings();
+		settings.put(TOOLCHAIN_FILE, toolChainFile.getPath().toString());
+		try {
+			settings.flush();
+		} catch (BackingStoreException e) {
+			Activator.log(e);
 		}
 	}
 
diff --git a/core/org.eclipse.cdt.core/src/org/eclipse/cdt/core/build/CBuildConfiguration.java b/core/org.eclipse.cdt.core/src/org/eclipse/cdt/core/build/CBuildConfiguration.java
index f9222e48b46..2c2e14cd68c 100644
--- a/core/org.eclipse.cdt.core/src/org/eclipse/cdt/core/build/CBuildConfiguration.java
+++ b/core/org.eclipse.cdt.core/src/org/eclipse/cdt/core/build/CBuildConfiguration.java
@@ -417,7 +417,8 @@ public abstract class CBuildConfiguration extends PlatformObject
 	}
 
 	protected Path findCommand(String command) {
-		if (Platform.getOS().equals(Platform.OS_WIN32) && !command.endsWith(".exe")) { //$NON-NLS-1$
+		if (Platform.getOS().equals(Platform.OS_WIN32)
+				&& !(command.endsWith(".exe") || command.endsWith(".bat"))) { //$NON-NLS-1$ //$NON-NLS-2$
 			command += ".exe"; //$NON-NLS-1$
 		}