I have searched through google and SO for possible answers to this question, but can only find small bits of information scattered around the place, most of which appear to be p
Ask the user.
Ask the user.
Ask the user.
Ask the user (notice a trend here?).
Typically, patch, if the application is of any significant size.
As far as the "ask the user" responses go, it doesn't mean always prompt them every single time. Instead, give them the option to set what they should be prompted for and what should just be done invisibly (and the first time a given thing occurs, ask them what should be done in the future, and remember that). This shouldn't be very difficult and you gain a lot of goodwill from a larger portion of your user base, since it's very hard to have fixed settings suit the desires of everyone who uses your app. When in doubt, more options are better than less - especially when they're the kind of option that's fairly trivial to code.