diff --git a/spring-boot-tools/spring-boot-gradle-plugin/src/main/groovy/org/springframework/boot/gradle/task/RunApp.java b/spring-boot-tools/spring-boot-gradle-plugin/src/main/groovy/org/springframework/boot/gradle/task/RunApp.java
index db885b0ef06..46c48559a77 100644
--- a/spring-boot-tools/spring-boot-gradle-plugin/src/main/groovy/org/springframework/boot/gradle/task/RunApp.java
+++ b/spring-boot-tools/spring-boot-gradle-plugin/src/main/groovy/org/springframework/boot/gradle/task/RunApp.java
@@ -52,8 +52,7 @@ public class RunApp extends DefaultTask {
 			SourceDirectorySet resources = main.getResources();
 			allResources.addAll(resources.getSrcDirs());
 			outputs = main.getOutput().getResourcesDir();
-		}
-		else {
+		} else {
 			outputs = null;
 		}
 
@@ -80,11 +79,16 @@ public class RunApp extends DefaultTask {
 					getLogger().info("Found main: " + mainClass);
 				}
 				if (outputs != null) {
-					// Special case: this file causes logback to worry that it has been
-					// configured twice, so remove it from the target directory...
-					File logback = new File(outputs, "logback.xml");
-					if (logback.exists()) {
-						logback.delete();
+					// remove duplicates from resources and build
+					for (File directory : allResources) {
+						if (directory.isDirectory()) {
+							for (String name : directory.list()) {
+								File file = new File(outputs, name);
+								if (file.exists() && file.canWrite()) {
+									getProject().delete(file);
+								}
+							}
+						}
 					}
 				}
 				exec.exec();
@@ -100,8 +104,7 @@ public class RunApp extends DefaultTask {
 		getLogger().info("Looking for main in: " + main.getOutput().getClassesDir());
 		try {
 			return MainClassFinder.findMainClass(main.getOutput().getClassesDir());
-		}
-		catch (IOException ex) {
+		} catch (IOException ex) {
 			throw new IllegalStateException("Cannot find main class", ex);
 		}
 	}
diff --git a/spring-boot-tools/spring-boot-maven-plugin/src/main/java/org/springframework/boot/maven/RunMojo.java b/spring-boot-tools/spring-boot-maven-plugin/src/main/java/org/springframework/boot/maven/RunMojo.java
index c840664fe94..5ffccaebc58 100644
--- a/spring-boot-tools/spring-boot-maven-plugin/src/main/java/org/springframework/boot/maven/RunMojo.java
+++ b/spring-boot-tools/spring-boot-maven-plugin/src/main/java/org/springframework/boot/maven/RunMojo.java
@@ -37,6 +37,7 @@ 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;
 
@@ -62,10 +63,7 @@ public class RunMojo extends AbstractMojo {
 
 	/**
 	 * Add maven resources to the classpath directly, this allows live in-place editing or
-	 * resources. Since resources will be added directly, and via the target/classes
-	 * folder they will appear twice if ClassLoader.getResources() is called. In practice
-	 * however most applications call ClassLoader.getResource() which will always return
-	 * the first resource.
+	 * resources.
 	 */
 	@Parameter(property = "run.addResources", defaultValue = "true")
 	private boolean addResources;
@@ -185,6 +183,9 @@ public class RunMojo extends AbstractMojo {
 		catch (MalformedURLException ex) {
 			throw new MojoExecutionException("Unable to build classpath", ex);
 		}
+		catch (IOException ex) {
+			throw new MojoExecutionException("Unable to build classpath", ex);
+		}
 	}
 
 	private void addUserDefinedFolders(List<URL> urls) throws MalformedURLException {
@@ -195,16 +196,25 @@ public class RunMojo extends AbstractMojo {
 		}
 	}
 
-	private void addResources(List<URL> urls) throws MalformedURLException {
+	private void addResources(List<URL> urls) throws MalformedURLException, IOException {
 		if (this.addResources) {
 			for (Resource resource : this.project.getResources()) {
-				urls.add(new File(resource.getDirectory()).toURI().toURL());
-			}
-			// Special case: this file causes logback to worry that it has been configured
-			// twice, so remove it from the target directory...
-			File logback = new File(this.classesDirectory, "logback.xml");
-			if (logback.exists() && logback.canWrite()) {
-				logback.delete();
+				File directory = new File(resource.getDirectory());
+				urls.add(directory.toURI().toURL());
+				if (directory.isDirectory()) {
+					// Remove duplicates from the target directory...
+					for (String name : directory.list()) {
+						File file = new File(this.classesDirectory, name);
+						if (file.exists() && file.canWrite()) {
+							if (file.isDirectory()) {
+								FileUtils.deleteDirectory(file);
+							}
+							else {
+								file.delete();
+							}
+						}
+					}
+				}
 			}
 		}
 	}