@mikero
You are right, the script goes into memory for the time being, however, once the script is finished, or forced to exit(by an outside force), OFP trashes it and re-reads it once the script is executed. I've tested it in-game with a small example program. I have two scripts, one that is a loop and executes and empty script file once every couple of seconds. I used the program to hold script file and write data to it, such as a hint command. When the looping script repeats the execute command, the hint command pops up in the game. This shows that the scripts are not held in long-term memory.
Well, the idea was to create an easy java editor for this. You could "insert", so to speak, scripts at certain times in the game, or even block OFP from running certain scripts, and even parts within a script. The tool would be mainly meant for "during play" editing of scripts and such. In the case of a single play mission, the mission maker could create his own "programme" for which he has planned for the user. Certain options that could not be easily used in scripting can be easily manipulated from outside OFP.. From what I understand fwatch only allows you to do certain things from within the scripts, for example, the 30 or so commands provided with it.
Btw, if you want fwatch to work on linux servers, use a program known as "Wine" it can be easily found online, just search into google, "Wine Linux".