why the rule "verb comma verb" does not appy in this sentence ?
Er ist ein Mann,der weiß,was er will I thought they were suppost to be like this following 'Das Dorf, in dem ich wohne,ist klein
I believe that before the spelling reform you had to use a comma, as you said. I'm not sure if you can officially leave it out today (EDIT: no you can't), or if it's just something many people do wrong because they copy their comma rules from English (that kind of thing does happen).
EDIT: I forgot to mention that I was only referring to the second comma. Sorry! "Er ist ein Mann, der..." very much needs a comma; it's just the "der weiß, was er will" that I think I sometimes see without one (incorrectly).
...so I looked it up, and you still need both commas in there. I'll have a try at yet another explanation to maybe make it clearer:
The main clause you can reduce the whole sentence to is "Er ist ein Mann". It then gets two "follow-up definitions":
The relative close that follows needs a comma in German: "Er ist ein Mann, der..." (as opposed to English: "He is a man who..."). E.g.: "Er ist ein Mann, der viel weiß / der gerne liest." "He is a man who knows a lot / who likes to read."
Now in this case, there's a second relative close that depends on the "weiß / knows" and "defines" it further: "He knows what he wants / what an umlaut is / what I did last summer." In German, we need a comma here as well: "Er weiß, was er will / was ein Umlaut ist / was ich letzten Sommer getan habe." (In the entry for "wissen", the Duden gives this example: "Sie weiß, was sie will.")
If you like, you can imagine the whole thing as a construction of boxes: The whole sentence is a big box. In it, there's "Er ist ein Mann (...).", and in place of the "(...)" there's a smaller box. That box contains "der weiß (...)", and that box contains a smaller box with "was er will" in it.
(As guitarluehe pointed out, you can't remove the "der weiß"-box without removing the "was er will"-box as well, because they're inside one another.)
In "Das Dorf, in dem ich wohne, ist klein", the big box contains "Das Dorf (...) ist klein.", and there's only one smaller box in it: "in dem ich wohne" - so "in dem ich wohne" is an insertion and thus needs commas around it. (Again: different in English: "The village that I live in is small.")
Das Dorf, in dem ich wohne, ist klein. If you leave the sentence "in dem ich wohne" the rest still works. It has a meaning and it is grammatically ok.
"Er ist ein Mann was er will" does not work. It has no meaning. If you regard "der weiß" as a relative clause, the German Grammar says that necessary relative clauses are not separated from the main sentence by comma. And that is the difference. First example necessary relative clause, second example not necessary. The fact that you live there could well be in another sentence. But I don't have the slightest problem with the commas in "Er ist ein Mann,der weiß,was er will". They do no harm. It would be a minor error even for a native speaker.
So my recommendation is sticking to the basic comma rules and put the rest of the commas where it is necessary to catch the meaning. In the following sentence there are two possibilities to put the comma "Peter erbt das Haus nicht aber Rainer". In one position position of the comma Peter gets the house, in the other Rainer. This is a typical example that the comma should help to understand the meaning of a sentence.