<outputConfigurations>
    <outputConfiguration>
        <name>custom-java</name>
        <outputDirectory>./src/main/java</outputDirectory>
        <overrideExistingResources>false</overrideExistingResources>
        <cleanUpDerivedResources>false</cleanUpDerivedResources>
    </outputConfiguration>
</outputConfigurations>

<plugin>
   <groupId>org.apache.maven.plugins</groupId>
      <artifactId>maven-clean-plugin</artifactId>
      <version>2.5</version>
      <executions>
         <execution>
            <phase>clean</phase>
            <goals>
               <goal>clean</goal>
            </goals>
            <configuration>
		<filesets>
			 <fileset>
				<directory>src/main/generated/</directory>
				<includes>
					<include>**/*</include>
				 </includes>
			</fileset>
		</filesets>
            </configuration>
      </execution>
      </executions>
</plugin>

...

<outputDirectory>src/main/generated</outputDirectory>

public Class<? extends JavaIoFileSystemAccess> bindJavaIoFileSystemAccess() {
    return OutputConfigurationAwareFileSystemAccess.class;	
}

package my.package.common.output;

import java.io.BufferedOutputStream;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.io.OutputStreamWriter;

import org.eclipse.xtext.generator.JavaIoFileSystemAccess;
import org.eclipse.xtext.generator.OutputConfiguration;
import org.eclipse.xtext.util.RuntimeIOException;

import com.google.common.io.ByteStreams;

public class OutputConfigurationAwareFileSystemAccess extends JavaIoFileSystemAccess {

	@Override
	public void generateFile(String fileName, String outputName, CharSequence contents) throws RuntimeIOException {
		OutputConfiguration outputConfig = getOutputConfig(outputName);
		File file = getFile(fileName, outputName);
		if (!createFolder(file.getParentFile(), outputConfig)) {
			return; // folder does not exist
		}
		
		if (!file.exists() || outputConfig.isOverrideExistingResources()) {
			try {
				String encoding = getEncoding(getURI(fileName, outputName));
				OutputStreamWriter writer = new OutputStreamWriter(new FileOutputStream(file), encoding);
				try {
					writer.append(postProcess(fileName, outputName, contents, encoding));
					if (isWriteTrace()) {
						generateTrace(fileName, outputName, contents);
					}
				} finally {
					writer.close();
				}
			} catch (IOException e) {
				throw new RuntimeIOException(e);
			}
		}
	}

	@Override
	public void generateFile(String fileName, String outputName, InputStream content) throws RuntimeIOException {
		OutputConfiguration outputConfig = getOutputConfig(outputName);
		File file = getFile(fileName, outputName);
		if (!createFolder(file.getParentFile(), outputConfig)) {
			return; // folder does not exist
		}

		if (!file.exists() || outputConfig.isOverrideExistingResources()) {
			try {
				OutputStream out = new BufferedOutputStream(new FileOutputStream(file));
				try {
					ByteStreams.copy(content, out);
				} finally {
					try {
						out.close();
					} finally {
						content.close();
					}
				}
			} catch (IOException e) {
				throw new RuntimeIOException(e);
			}
		}
	}

	protected boolean createFolder(File parent, OutputConfiguration outputConfig) {
		if (parent != null && !parent.exists() && outputConfig.isCreateOutputDirectory() && !parent.mkdirs()) {
			throw new RuntimeIOException("Could not create directory " + parent);
		}
		return parent != null && parent.exists();
	}

}