The Peace Establishment act of 1802 did in fact cut the military down to a token force. Jefferson was not a big fan of standing armies and navies. The act basically neutered the Navy (which was a bastion of Northeastern Federalist support -his political enemies in party politics) which developed significanly in the 1790s during the Naval war with France which a large number of frigates, super-frigates (Constitution, Constellation, etc), and built and bought numerous sloops, schooner, brigs, and ships. Most of the vessels were sold off after the act of 1802 and the navy was downsized bumping out all but the most experienced and politically connected officers and men. The army was the same deal, although it had been small in the 1790s to begin with. In terms of military command experience & Lewis & Clark, they were both officers, but that doesn't mean they were active officers at the time they were recruited to go. Also their mission was a special one ordered by the President himself If I'm not mistaken, and even if Lewis & Clark were not "regular" army (what little their was of it at the time) they could have been state militia officers at some point, or in state armies (they had them until 1787 --articles of confederation period). Jefferson cut the army because he was more isolationist than the Adams administration or Washington's (where pro-trade, foreign treaty supporters like Adams and Alexander Hamilton held sway).
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