Address review comments.

core/src/main/java/hudson/Util.java

@@ -623,6 +623,7 @@ public class Util {
     // TODO JENKINS-60563 remove MD5 from all usages in Jenkins
     @SuppressFBWarnings(value = "WEAK_MESSAGE_DIGEST_MD5", justification =
             "This method should only be used for non-security applications where the MD5 weakness is not a problem.")
+    @Deprecated
     private static MessageDigest getMd5() throws NoSuchAlgorithmException {
         return MessageDigest.getInstance("MD5");
     }

core/src/main/java/jenkins/model/RunIdMigrator.java

@@ -322,7 +322,7 @@ public final class RunIdMigrator {
         new RunIdMigrator().unmigrateJobsDir(jobs);
     }
 
-    @SuppressFBWarnings(value = "PATH_TRAVERSAL_IN", justification = "Only used as an command-line process.")
+    @SuppressFBWarnings(value = "PATH_TRAVERSAL_IN", justification = "Only invoked from the command line as a standalone utility")
     private static File constructFile(String arg) {
         return new File(arg);
     }