Methodology as a Body of Methods?
Words don't have a fixed meaning, and dictionaries only follow usage here. That is what is happening here.

The “classical” meaning of methodology is (my own words): a branch of epistemology that studies scientific methods, i.e. the systematic, theoretical analysis of the methods applied in science. (Epistemology, in turn, is a branch of philosophy dealing with knowledge).

This classical meaning is what the eponym Wikipedia article discusses (WP being an encyclopedia, not a dictionary, it doesn't have to list all meanings of a given word). It's also what one of the Merriam-Webster definitions says:


  the analysis of the principles or procedures of inquiry in a particular field




Now, language evolves, and in addition to this “classical” meaning of methodology (which is, in that sense, a mass noun), a second meaning is developing. This new meaning is “a collection of methods used in conjunction”, as you noted.

Now, as with every language evolution, some people complain about it (and the Wikipedia article on Methodology is clearly written from this point of view; see “Methodology as a buzzword” section). The Wiktionary article goes on to say:


  Etymologically, methodology refers to the study of methods. Thus the use of methodology as a synonym for methods (or other simple terms such as means, technique, or procedure) is proscribed as both inaccurate and pretentious.


Well, sod them to Hades! It is clear that this newer meaning is abundantly used in the academic literature these days, and can thus be considered acceptable.



(If you've never seen it, this wonderful tirade by Stephen Fry should cure you of prescriptivism. It is delightful to hear… “They're no more guardians of language than the Kennel Club is the guardian of dogkind.”)