I tried to see if the same procedure would execute by writing an anonymous PL/SQL block and it did.
This is what SQL Developer (4.0.2) was showing me...The package clearly defines a procedure, but it is not visible in the run dialog box, instead SQL Developer is reporting an empty package definition (no public members).
I checked the DB version and the results were 126.96.36.199.0.
Thinking this is a 12c related problem, I connected to a different database that has not been upgraded, still at 11gR2 level, lo and behold, my procedure was visible in the run dialogue again. Definitely a 12c related issue then.
The DBA suggested that I try SQL Developer 4.1 Early Adopter to see if that helps. It did! Looks like SQL Developer 4.0.x is not fully compatible with 188.8.131.52 version of the database.
The fixed bug list confirms this...
Looking deeper into the bug it only seems to affect 184.108.40.206.0 database version, if you are on 220.127.116.11.0, this problem does not show up.
So there you go, if you got the latest DB version, the latest SQL Developer fixes this little problem!