The Commando program for SR is about to enter a period of flux, and some things may change...but DM summed things up pretty much...
The numbering scheme for Shadowrun Missions is as follows:
SRM99-88X
SRM = Shadowrun Missions, 'natch
99 = The current story arc. 00 is for all the Demo/Intro adventures, which help introduce new characters/players to the campaign and/or game system. These adventures will be available at least for the foreseeable future - if we find that we need to change them, they'll still have a 00 in the front.
01 is to indicate an adventure that occurs during the first story arc, which will be two years in length - this story arc overall is called "Rose Croix" and will deal with the rise, competition, and fall (?) of a new medical service company to compete against DocWagon. The players will determine by the end of the story arc whether Rose Croix remains as a competitor and viable corporation in Seattle.
88 = Sequential adventure number. This is a one-up number that will show the order that the adventures should be played in. You don't HAVE to play them in this order, but as with a story, if you start playing too many of them out of order, you might learn things ahead of time or become confused. If you're good at separating character knowledge from player knowledge, this shouldn't be a problem - you can play #7 one day, then play #10, leaving a gap of time between 7 and 10, and then go back and play #8 as if your character were having a flashback episode...or just play 8 anyways after 10 and don't worry about it - it's up to you, the player...
since i know we'll never get above 90 adventures over a two year period, any adventure in the 90s means that it is a stand-alone adventure - you do not have to play these in any particular order, unless the adventure states so.
X = Reserved character. Right now, we are using A and B to represent the adventure itself (A) and the handouts (B). If we need more expansion, we have more letters to use...
so, SRM01-05 would be adventure #5 in the first story arc, whereas SRM01-95 would be a stand alone adventure, not part of the story arc, but meant to be played during the same 2-yr period, and is the 5th one.
The numbering is really to help keep me organized and be able to schedule events with the conventions - they help you to quickly recognize what order you play things in, if you want to stay "current"...you have to know how to count, though...