Fix a bug in path handling

This patch fixes the convertion from URL to path so that paths containing the '+' character are not converted to ' '.
Without it, picard.jar can't be placed in a path where one directory has a '+' in its name (and that happens on Debian builders)

src/java/picard/cmdline/ClassFinder.java

@@ -30,7 +30,8 @@
 import java.io.IOException;
 import java.net.URL;
 import java.net.URLClassLoader;
-import java.net.URLDecoder;
+import java.net.URI;
+import java.net.URISyntaxException;
 import java.util.*;
 import java.util.zip.ZipEntry;
 import java.util.zip.ZipFile;
@@ -63,8 +64,8 @@ public ClassFinder(final File jarFile) throws IOException {
         // but the jarPath is remembered so that the iteration over the classpath skips anything other than
         // the jarPath.
         jarPath = jarFile.getCanonicalPath();
-        final URL[] urls = {new URL("file", "", jarPath)};
-        loader = new URLClassLoader(urls, Thread.currentThread().getContextClassLoader());
+        final URL[] urls = {new File(jarPath).toURI().toURL()};
+    loader = new URLClassLoader(urls, Thread.currentThread().getContextClassLoader());
     }
 
     /** Convert a filename to a class name by removing '.class' and converting '/'s to '.'s. */
@@ -95,9 +96,14 @@ public void find(String packageName, final Class<?> parentType) {
         while (urls.hasMoreElements()) {
             try {
                 String urlPath = urls.nextElement().getFile();
-                urlPath = URLDecoder.decode(urlPath, "UTF-8");
-                if ( urlPath.startsWith("file:") ) {
-                    urlPath = urlPath.substring(5);
+                // convert URL to URI
+                // http://bugs.java.com/bugdatabase/view_bug.do?bug_id=4466485
+                // using URLDecode does not work if urlPath has a '+' character
+                try {
+                    URI uri = new URI(urlPath);
+                   urlPath = uri.getPath();
+                } catch (URISyntaxException e) {
+                    log.warn("Cannot convert to URI the " + urlPath + " URL");
                 }
                 if (urlPath.indexOf('!') > 0) {
                     urlPath = urlPath.substring(0, urlPath.indexOf('!'));
@@ -180,4 +186,4 @@ protected void handleItem(final String name) {
     public Set<Class<?>> getClasses() {
         return this.classes;
     }
-}
+}