Fixing javadocs and adding missing package javadocs.
Also marked a few packages and classes as deprecated.

Change-Id: I8629ad001f218f92c35721daa3b7c0ebe0916c27
diff --git a/apps/optical/src/main/java/org/onlab/onos/optical/cfg/PktOptLink.java b/apps/optical/src/main/java/org/onlab/onos/optical/cfg/PktOptLink.java
index f76a058..fb1d44b 100644
--- a/apps/optical/src/main/java/org/onlab/onos/optical/cfg/PktOptLink.java
+++ b/apps/optical/src/main/java/org/onlab/onos/optical/cfg/PktOptLink.java
@@ -18,6 +18,7 @@
 /**
  * Packet-optical link Java data object.
  */
+@Deprecated
 class PktOptLink {
     private String srcNodeName;
     private String snkNodeName;