Fix javadoc warnings

Author: ctrueden

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

@@ -122,8 +122,8 @@ private void log(final String msg) {
 	// -- Helper Class --
 
 	/**
-	 * {@link StreamFactory} implementation for writing an annotation.
-	 *
+	 * {@link AbstractIndexWriter.StreamFactory} implementation for writing an
+	 * annotation.
 	 */
 	private static class AnnotationStreamFactory implements StreamFactory {
 

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

@@ -66,7 +66,6 @@ public class Index<A extends Annotation> implements Iterable<IndexItem<A>> {
 	 * 
 	 * @param annotation the annotation type
 	 * @return the index
-	 * @throws IOException
 	 */
 	public static <A extends Annotation> Index<A> load(final Class<A> annotation)
 	{
@@ -82,7 +81,6 @@ public static <A extends Annotation> Index<A> load(final Class<A> annotation)
 	 * @param loader the class loader to use when loading {@link Class}-type
 	 *          annotation fields
 	 * @return the index
-	 * @throws IOException
 	 */
 	public static <A extends Annotation> Index<A> load(final Class<A> annotation,
 		final ClassLoader loader)

src/main/java/org/scijava/annotations/legacy/LegacyReader.java

@@ -314,8 +314,10 @@ protected final Object readWithoutClassDesc() throws IOException {
 			return o;
 		}
 
+		/**
+		 * @throws IOException If something goes wrong reading the map.
+		 */
 		protected Object readExtra(Map<String, Object> o) throws IOException {
-
 			return o;
 		}
 	}

src/main/java/org/scijava/util/CheckSezpoz.java

@@ -78,7 +78,7 @@ private CheckSezpoz() {
 	 * @param checkJars whether to inspect .jar components of the CLASSPATH
 	 * @return false, when the annotation processor had to be run
 	 * @throws IOException
-	 * @see {@link EclipseHelper}
+	 * @see EclipseHelper
 	 */
 	@Deprecated
 	public static boolean check(final boolean checkJars) throws IOException {
@@ -92,7 +92,7 @@ public static boolean check(final boolean checkJars) throws IOException {
 	 * @param file the CLASSPATH component (.jar file or directory)
 	 * @return false, when the annotation processor had to be run
 	 * @throws IOException
-	 * @see {@link EclipseHelper}
+	 * @see EclipseHelper
 	 */
 	@Deprecated
 	public static boolean check(final File file) throws IOException {
@@ -107,7 +107,7 @@ public static boolean check(final File file) throws IOException {
 	 * @param classes the CLASSPATH component directory
 	 * @return false, when the annotation processor had to be run
 	 * @throws IOException
-	 * @see {@link EclipseHelper}
+	 * @see EclipseHelper
 	 */
 	@Deprecated
 	public static boolean checkDirectory(final File classes) throws IOException {
@@ -127,7 +127,7 @@ public static boolean checkDirectory(final File classes) throws IOException {
 	 * @param source the <i>src/main/java/<i> directory where Maven expects the
 	 *          <i>.java</i> files
 	 * @param youngerThan the date/time when we last checked
-	 * @see {@link EclipseHelper}
+	 * @see EclipseHelper
 	 */
 	@Deprecated
 	public static boolean checkDirectory(final File classes, final File source,
@@ -144,7 +144,7 @@ public static boolean checkDirectory(final File classes, final File source,
 	 * </p>
 	 * 
 	 * @param file the <i>.jar</i> file
-	 * @see {@link EclipseHelper}
+	 * @see EclipseHelper
 	 */
 	@Deprecated
 	public static void checkJar(final File file) throws IOException {
@@ -158,7 +158,7 @@ public static void checkJar(final File file) throws IOException {
 	 * @param classes the output directory
 	 * @param sources the directory containing the source files
 	 * @return whether anything in {@code META-INF/annotations/*} changed
-	 * @see {@link EclipseHelper}
+	 * @see EclipseHelper
 	 */
 	@Deprecated
 	public static boolean fix(final File classes, final File sources) {

src/main/java/org/scijava/util/CombineAnnotations.java

@@ -45,14 +45,20 @@ public class CombineAnnotations
 {
 
 	/**
-	 * @deprecated Use {@link org.scijava.annotations.AnnotationCombiner#CombineAnnotations()} instead.
+	 * @deprecated Use
+	 *             {@link org.scijava.annotations.AnnotationCombiner#AnnotationCombiner()}
+	 *             instead.
+	 * @throws IOException
 	 */
 	@Deprecated
 	public CombineAnnotations() throws IOException {}
 
 	private AnnotationCombiner combiner = new AnnotationCombiner();
+
 	/**
-	 * @deprecated Use {@link org.scijava.annotations.AnnotationCombiner#combine()} instead.
+	 * @deprecated Use
+	 *             {@link org.scijava.annotations.AnnotationCombiner#combine(File)}
+	 *             instead.
 	 */
 	@Deprecated
 	public void combine() throws IOException, ClassNotFoundException {