Shawn, I suspect that the Prouty-Dana involvement was over changes to the nautical signal flags used aboard ship...hoisted. Members of the USN and related maritime services (Marines, Revenue Marine) who "went South" were of course familiar with the existing flag code (the "secret" meanings of those flags, whether or not they actually took a copy of the code book ), so changes had to be made in the North. The quickest simple ways would have been to change the numerical value assigned to a flag (that is, "scramble" the meanings or flags), or retain the flags and change the code book meanings, which took longer. So a temporary change was made, then another, and in no time confusion was starting to create operational problems, and a new look -- a complete change -- was in order. The men who went South had to start from scratch. They used most of the old signal flags, but slipped in a few different ones, and they "scrambed" the numerical values signified. As for a code book, they started with the bare minimum of essential terms and then overhauled the system about a year or so into the war.

Several different systems were introduced in the South, along the coasts, using hoisted flags, balls, or the like, raised on a fixed pole and keyed in meaning to a code list or code book. In other words, a land-based, fixed system similar to what they'd experienced afloat.They were later superseded.

The system I'm most interested in is the one introduced by US Army assistant surgeon A.J. Myer of NY, just before the war. He proved the system with the aid of a Georgia-born West Point engineer, E. Porter Alexander, to the satisfaction of a board headed by Col. RE Lee. As a result, the War Dept made Myer "Signal Officer of the Army" (a one-man show), but that's the date the Signal Corps considers its birthday (even though it was a provisional, wartime organization when set up in 1863). Alexander "went South" and started a system at First Manassas (Bull Run) using the Myer system he had learned and helped to develop. That system used a single flag (or two torches at night, one on the ground for reference and one replacing the "waved" flag on the staff) and spelled out words letter by letter. It was mockingly referred to by at least one man in the North as "wig-wag." After the war, that term caught on (sort of like 20th Century "Coke" for "Coca-Cola," which was initially resisted). It was adopted, with appropriate variations in meaning, by both armies as their standard. And that's the system I'm studying.

I'll try to watch out for Proutys -- must have had enough for a small brigade!