Allow bootWar to package webapp resources in dirs that overlap loader

Previously, the presence of a src/main/webapp/org directory would
cause the execution of BootWar to fail due to an attempt to write
a duplicate org/ entry to the zip output stream.

This commit updates BootZipCopyAction so that FileTreeElements that
match a directory entry created while writing the loader classes are
skipped.

Closes gh-8972

spring-boot-tools/spring-boot-gradle-plugin/src/test/java/org/springframework/boot/gradle/tasks/bundling/BootWarTests.java

@@ -16,6 +16,7 @@
 
 package org.springframework.boot.gradle.tasks.bundling;
 
+import java.io.File;
 import java.io.IOException;
 import java.util.jar.JarFile;
 
@@ -76,4 +77,21 @@ public class BootWarTests extends AbstractBootArchiveTests<BootWar> {
 		}
 	}
 
+	@Test
+	public void webappResourcesInDirectoriesThatOverlapWithLoaderCanBePackaged()
+			throws IOException {
+		File webappFolder = this.temp.newFolder("src", "main", "webapp");
+		File orgFolder = new File(webappFolder, "org");
+		orgFolder.mkdir();
+		new File(orgFolder, "foo.txt").createNewFile();
+		getTask().from(webappFolder);
+		getTask().setMainClass("com.example.Main");
+		getTask().execute();
+		assertThat(getTask().getArchivePath().exists());
+		try (JarFile jarFile = new JarFile(getTask().getArchivePath())) {
+			assertThat(jarFile.getEntry("org/")).isNotNull();
+			assertThat(jarFile.getEntry("org/foo.txt")).isNotNull();
+		}
+	}
+
 }