1st I am ONLY looking for RAW answers, I have plenty of my own logical reasonings for the answer should be what I think it should be so I don't need more of those. Please read the whole question to get a full understanding of why the question is being asked.
In UA, under Variant Classes the rules state:
"...Each fully detailed variant has entries for one or more of the following topics. If an entry does not appear, use the material for the class as presented in the Player’s Handbook."
Class Skills: Additions or subtractions from the class skill list, and/or changes in the number of skill points gained per level.
Now when we skip down to the Cloistered Cleric we see (emphasis mine):
Class Skills: The cloistered cleric’s class skill list includes Decipher Script, Speak Language, and all Knowledge skills (from the Knowledge domain, see below). The cloistered cleric gains skill points per level equal to 6 + Int modifi er (and has this number ×4 at 1st level).
The wording is important because it does not say "Add" or "Replace" it just says includes. If we go to the dictionary it says: Includes: "comprise or contain as part of a whole". So we see that this wording doesn't explicitly exclude the original clerics skills but it also doesn't explicitly include them and is at best ambiguous in itself.
So, to solve the mystery, lets compare it to another class:
Fighter Variant: Thug has the following entry (again, Emphasis Mine):
Class Skills: Add the following skills to the fighter’s class skill list: Bluff, Gather Information, Knowledge (local), and Sleight of Hand. The thug gains skill points per level equal to 4 + Int modifier (and has this number ×4 at 1st level).
The other variant classes either follow this same "Add/Remove" skills or say replace skill X with skill y. So, why is the Cloistered Cleric different? The only conclusion that could be drawn from the RAW is that the list ONLY includes those listed and now excludes those from the original Cleric's list. Of course, the flavor behind the Cloistered Cleric contradicts this so I believe that the RAI was for them to be ADDED to the list.
Bottom Line: RAW, Does the Cloistered Cleric's Skill list include the original Cleric's Skills as well (Heal, Concentration, etc) or does it now ONLY include the new list (Decipher Script, Speak Language & all Knowledges)? Has this been errata'd or addressed by WotC elsewhere?