Documentation cleanup (#612)

* Added the `@Deprecated` tag to instances where is was mentioned in documentation, but not for the actual code itself.

Changed one documentation link pointing at a non-existing item.

* As per PR suggestion.

(cherry picked from commit 196081a317)

common/common-io/src/main/java/com/twelvemonkeys/io/FilenameMaskFilter.java

@@ -65,6 +65,7 @@ import java.io.FilenameFilter;
  * @see WildcardStringParser
  * @deprecated
  */
+@Deprecated
 public class FilenameMaskFilter implements FilenameFilter {
 
      // TODO: Rewrite to use regexp, or create new class

common/common-io/src/main/java/com/twelvemonkeys/io/LittleEndianDataInputStream.java

@@ -442,6 +442,7 @@ public class LittleEndianDataInputStream extends FilterInputStream implements Da
      * @see        java.io.BufferedReader#readLine()
      * @see        java.io.DataInputStream#readLine()
      */
+    @Deprecated
     public String readLine() throws IOException {
         DataInputStream ds = new DataInputStream(in);
         return ds.readLine();