Having one or two batch scripts to help build the game, or run the interpreter in "no resource.map only loose files" mode is as streamlined as they got at the time.
So I'd say copying the rough structure of LSL2 or 3 might be a reasonable starting point. That is, put each resource type into its own directory for clarity. To play, have a script copy them all to a test directory including an interpreter and run it from there. Another script may be used to compile all .sc files in the src folder to script.# and text.# in the script directory. System scripts (255 and anything 900 or higher) go in the system directory along with things like drivers. interpreters, and any fonts and cursors that aren't specific to the game.
SC can take a @redo file, a straight list of filenames without extensions, and redo.bat in LSL2 and 3 uses that.
They apparently had the whole game on the root of a drive, so lines like copy \system\classdef would work. This happily matches what you'd get if you opened DOSBox and mounted your project folder.
