Caboodle is derived from the phrase "Kit and Caboodle". Kit and caboodle is a phrase that evolved over time. Most recently from the earlier phrase "kit and boodle". Boodle (or Buddle) is an old word, and probably evolved from the Dutch "boedel" meaning a crowd or bunch. "The whole boodle" was heard as long ago as the early 19th century.
Kit is also a time honored word with many meanings, one of which is a collection of tools or possessions that a person might carry with them. "The whole kit" was used by 1785.
Caboodle is essentially a nonsense word, and is perhaps a contraction or rhyme of "kit and boodle".
Stephen Crane's "The Red Badge of Courage" contains it: "Of course it might happen that the hull (whole) kit and boodle might start and run, if any big fighting came first-off.