Alright I have always accepted the answer of it's impossible to open a program on a local machine through javascript or html due to the obvious security vulnerabilities. However, the best solution we can find right now to a problem with a browser based POS system is to launch a desktop application for certain things.
The reason i'm second guessing that it may be possible is because of magnetLinks(which i know little about other than that I click it and my browser prompts me whether it's okay to launch the application and all of a sudden uTorrent is running with the data loaded in it. We have root access to every machine that will be running this web application and can configure the machine in any way needed so running chrome with flags or whatever is an option, i would just prefer to avoid installing activeX objects.
Edit: I have seen another similar question, however; in this instance all of the machines running the application are configured, installed, and maintained by our company.