Fix annotation processing when running javac without -d <directory>

Samuel Inverso noticed, and Mark Hiner diagnosed, that compiling SciJava
plugins using javac without specifying an output directory will write the
annotation index into an incorrect location (instead of META-INF/json/ it
is written into the top-level directory).

This can be verified using a very simple example x1.java file:

-- snip --
import org.scijava.plugin.Plugin;
import org.scijava.plugin.SciJavaPlugin;

@plugin(type = SciJavaPlugin.class)
public class x1 implements SciJavaPlugin { }
-- snap --

The reason is that javac's DefaultFileManager will strip out any
subdirectory in the path passed to the createResource() method unless
an output directory is specified.

Work around that by detecting the situation and creating the subdirectory
explicitly.

This fixes imagej/imagej-launcher#22.

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

Author: dscho

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

@@ -32,7 +32,9 @@
 package org.scijava.annotations;
 
 import java.io.ByteArrayOutputStream;
+import java.io.File;
 import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStream;
@@ -62,6 +64,7 @@
 import javax.lang.model.util.Elements;
 import javax.lang.model.util.Types;
 import javax.tools.Diagnostic.Kind;
+import javax.tools.FileObject;
 import javax.tools.StandardLocation;
 
 import org.scijava.annotations.AbstractIndexWriter.StreamFactory;
@@ -234,10 +237,27 @@ public InputStream openInput(String annotationName) throws IOException {
 		@Override
 		public OutputStream openOutput(String annotationName) throws IOException {
 			final List<Element> originating = originatingElements.get(annotationName);
-			return filer.createResource(StandardLocation.CLASS_OUTPUT, "",
-				Index.INDEX_PREFIX + annotationName,
-				originating.toArray(new Element[originating.size()]))
-				.openOutputStream();
+			final String path = Index.INDEX_PREFIX + annotationName;
+			final FileObject fileObject = filer.createResource(StandardLocation.CLASS_OUTPUT, "",
+				path, originating.toArray(new Element[originating.size()]));
+
+			/*
+			 * Verify that the generated file is in the META-INF/json/ subdirectory;
+			 * Despite our asking for it explicitly, the DefaultFileManager will
+			 * strip out the directory if javac was called without an explicit
+			 * output directory (i.e. without <code>-d</code> option).
+			 */
+			final String uri = fileObject.toUri().toString();
+			if (uri != null && uri.endsWith("/" + path)) {
+				return fileObject.openOutputStream();
+			}
+			final String prefix = uri.substring(0, uri.length() - annotationName.length());
+			final File file = new File(prefix + path);
+			final File parent = file.getParentFile();
+			if (parent != null && !parent.isDirectory() && !parent.mkdirs()) {
+				throw new IOException("Could not create directory: " + parent);
+			}
+			return new FileOutputStream(file);
 		}
 
 		@Override