my 2 cents:

using versions is very handy when you want to incorporate the latest
version on a new page in your project, but don't want to go back and
regression test all the other pages in the application

i've got structure like:
- /jquery/
   -/1.1.8/
       - jquery.js
       - jquery.pack.js
   ..etc etc..
   -/1.2.6/
       - jquery.js
       - jquery.pack.js

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