Do not auto-detect Eclipse when calling the EclipseHelper as main class

There needs to be a way to force the EclipseHelper to index all it can,
even when it thinks it is not running inside Eclipse at all.

The best idea is to make this automatic when calling EclipseHelper as a
main class because we *know* that the developer wants to index the
annotations in this case, even if Eclipse Indigo has passed the class path
elements in a semi-random order.

Wished-for by Christian Dietz.

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

Author: dscho

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

@@ -97,11 +97,13 @@
  */
 public class EclipseHelper extends DirectoryIndexer {
 
+	private static final String FORCE_ANNOTATION_INDEX_PROPERTY = "force.annotation.index";
 	static Set<URL> indexed = new HashSet<URL>();
 	private boolean bannerShown;
 
 	private static boolean debug =
 		"debug".equals(System.getProperty("scijava.log.level"));
+	private boolean autoDetectEclipse = true;
 
 	private static void debug(final String message) {
 		if (debug) {
@@ -131,10 +133,13 @@ public static void updateAnnotationIndex(final ClassLoader loader) {
 			return;
 		}
 		EclipseHelper helper = new EclipseHelper();
+		if (Boolean.getBoolean(FORCE_ANNOTATION_INDEX_PROPERTY)) {
+			helper.autoDetectEclipse = false;
+		}
 		boolean first = true;
 		for (final URL url : ((URLClassLoader) loader).getURLs()) {
 			debug("Checking URL: " + url);
-			if (first) {
+			if (helper.autoDetectEclipse && first) {
 				if (!"file".equals(url.getProtocol()) ||
 					(!url.getPath().endsWith("/") && !url.getPath().contains("surefire")))
 				{
@@ -177,7 +182,7 @@ private void maybeIndex(final URL url, final ClassLoader loader) {
 			 * but crucially also the target/classes/ and target/test-classes/
 			 * directories which may need to be indexed.
 			 */
-			if (path.matches(".*/target/surefire/surefirebooter[0-9]*\\.jar")) try {
+			if (!autoDetectEclipse || path.matches(".*/target/surefire/surefirebooter[0-9]*\\.jar")) try {
 				final JarFile jar = new JarFile(path);
 				Manifest manifest = jar.getManifest();
 				if (manifest != null) {
@@ -286,6 +291,7 @@ else if (file.isDirectory()) {
 	 * </p>
 	 */
 	public static void main(final String... args) {
+		System.setProperty(FORCE_ANNOTATION_INDEX_PROPERTY, "true");
 		updateAnnotationIndex(Thread.currentThread().getContextClassLoader());
 	}