Use the ByteCodeAnalyzer to write the annotation index

Instead of loading the classes, we read the annotations directly from the
.class files. This has two advantages over the previous method:

1. We avoid polluting the ClassLoader with loaded classes (which can be
   problematic e.g. when ij1-patcher wants to patch the classes before
   loading them at a later stage).

2. It is no longer necessary for the dependencies of the classes to be
   on the class path (though that is only true for the classes, not for
   the annotations).

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

Author: dscho

src/main/java/org/scijava/annotations/DirectoryIndexer.java

@@ -41,6 +41,7 @@
 import java.net.MalformedURLException;
 import java.net.URL;
 import java.net.URLClassLoader;
+import java.util.Map;
 
 /**
  * Indexes a directory of classes.
@@ -88,18 +89,28 @@ else if (file.isFile()) {
 				final String className =
 					classNamePrefix + fileName.substring(0, fileName.length() - 6);
 				try {
-					final Class<?> clazz = loader.loadClass(className);
-					for (final Annotation a : clazz.getAnnotations()) {
-						add(a, className);
+					for (final Map.Entry<String, Map<String, Object>> entry : ByteCodeAnalyzer
+						.getAnnotations(file).entrySet())
+					{
+						final String annotationName = entry.getKey();
+						try {
+							if (!isIndexable(loader.loadClass(annotationName))) {
+								continue;
+							}
+						}
+						catch (ClassNotFoundException e) {
+							// fall back to the class loader that laoded the directory indexer
+							if (!isIndexable(Class.forName(annotationName))) {
+								continue;
+							}
+						}
+						add(entry.getValue(), annotationName, className);
 					}
-				} catch (NoClassDefFoundError e) {
-					System.err.println("Warning: could not load class '" + className + "' ("
-							+ e.getMessage() + "); skipping");
-				} catch (ClassNotFoundException e) {
-					System.err.println("Warning: could not load class '" + className + "'; skipping");
-				} catch (Throwable e){
-					System.err.println("Warning: could not load class '" + className + "' ("
-							+ e.getMessage() + "); skipping");
+				}
+				catch (Throwable e) {
+					System.err.println("Warning: could not load class '" + className +
+						"'; skipping");
+					e.printStackTrace();
 				}
 			}
 		}
@@ -116,7 +127,11 @@ protected synchronized <A extends Annotation> void add(final A annotation,
 
 	private static <A extends Annotation> boolean isIndexable(final A annotation)
 	{
-		return annotation.annotationType().getAnnotation(Indexable.class) != null;
+		return isIndexable(annotation.annotationType());
+	}
+
+	private static boolean isIndexable(final Class<?> annotationClass) {
+		return annotationClass.getAnnotation(Indexable.class) != null;
 	}
 
 	protected synchronized void write(final File directory) throws IOException {