Verify that inner classes are handled correctly

Test both the directory indexer and the annotation processor (the latter
in the integration test).

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>

Author: dscho

src/it/apt-test/src/main/java/org/scijava/annotation/its/Annotated.java

@@ -38,4 +38,7 @@
  * @author Johannes Schindelin
  */
 @CustomAnnotation(greeting = "Hey, what's up, doc?")
-public class Annotated { }
+public class Annotated {
+	@CustomAnnotation(greeting = "Howdy, stranger!")
+	public class Inner {}
+}

src/it/apt-test/src/test/resources/expect

@@ -1 +1 @@
-{"class":"org.scijava.annotations.its.Annotated","values":{"greeting":"Hey, what's up, doc?"}}
+{"class":"org.scijava.annotations.its.Annotated","values":{"greeting":"Hey, what's up, doc?"}}{"class":"org.scijava.annotations.its.Annotated$Inner","values":{"greeting":"Howdy, stranger!"}}

src/test/java/org/scijava/annotations/AnnotatedInnerClass.java

@@ -0,0 +1,45 @@
+/*
+ * #%L
+ * Annotation index (processor and index access library).
+ * %%
+ * Copyright (C) 2009 - 2013 Board of Regents of the University of Wisconsin-Madison.
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * 
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * 
+ * The views and conclusions contained in the software and documentation are
+ * those of the authors and should not be interpreted as representing official
+ * policies, either expressed or implied, of any organization.
+ * #L%
+ */
+
+package org.scijava.annotations;
+
+/**
+ * A simple class with an annotated inner class.
+ * 
+ * @author Johannes Schindelin
+ */
+public class AnnotatedInnerClass {
+
+	@Complex(simple = @Simple)
+	public class InnerClass {}
+}

src/test/java/org/scijava/annotations/DirectoryIndexerTest.java

@@ -34,6 +34,7 @@
 package org.scijava.annotations;
 
 import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertTrue;
 import static org.junit.Assume.assumeTrue;
 
@@ -83,7 +84,7 @@ public void testIndexer() throws Exception {
 			map.put(item.className(), item);
 		}
 
-		assertEquals(3, map.size());
+		assertEquals(4, map.size());
 		Complex a = map.get(AnnotatedA.class.getName()).annotation();
 		assertEquals("Hello, World!", a.simple().string1());
 
@@ -109,6 +110,9 @@ public void testIndexer() throws Exception {
 		assertEquals(-47, c.array1()[1]);
 		assertEquals(-53, c.array1()[2]);
 		assertEquals(-59, c.array1()[3]);
+
+		c = map.get(AnnotatedInnerClass.InnerClass.class.getName()).annotation();
+		assertNotNull(c);
 	}
 
 	public static String getResourcePath(final Class<?> clazz) {