Do not delete duplicate directories from main classpath

Before this change we were too aggressive in deleting duplicate resources
since directories might not have identical contents, and yet they were
being deleted anyway.

Fixes gh-614

spring-boot-tools/spring-boot-maven-plugin/src/main/java/org/springframework/boot/maven/RunMojo.java

@@ -37,7 +37,6 @@ import org.apache.maven.plugins.annotations.Mojo;
 import org.apache.maven.plugins.annotations.Parameter;
 import org.apache.maven.plugins.annotations.ResolutionScope;
 import org.apache.maven.project.MavenProject;
-import org.codehaus.plexus.util.FileUtils;
 import org.springframework.boot.loader.tools.AgentAttacher;
 import org.springframework.boot.loader.tools.MainClassFinder;
 
@@ -208,11 +207,11 @@ public class RunMojo extends AbstractMojo {
 			for (String name : directory.list()) {
 				File targetFile = new File(this.classesDirectory, name);
 				if (targetFile.exists() && targetFile.canWrite()) {
-					if (targetFile.isDirectory()) {
-						FileUtils.deleteDirectory(targetFile);
+					if (!targetFile.isDirectory()) {
+						targetFile.delete();
 					}
 					else {
-						targetFile.delete();
+						removeDuplicatesFromTarget(targetFile);
 					}
 				}
 			}