For sure, it's difficult. As you say, it probably can be done securely. It certainly needs to be done to provide users with a bridge for moving data from file systems into web apps and back and manipulating data from both sides of the bridge. It may require a special privilege, and in that case, for example for a trusted web app, it need be no more scary than a browser prompt: "allow this web application to open 'mydata.xls' in Excel?" with a "remember my choice for all files of this type from now on".