I have not yet faced this situation myself because I've always worked in more controlled environments (or on my own), but my general sense is that most people do one of the following things:
- make an executive decision about the oldest version of the module you'll support, put a run-time check for this in your code and fail gracefully if the minimum isn't met, and then write all your code so it'll work with that version. The version you pick depends on circumstances; it should not be the most recent, nor should it be so old as to really hamper your work.
- Bundle a separate version of the library with your application in such a way as not to conflict with the installed version. In the Perl world you can use PAR to help with this.
- Make certain functionality in your application optional. Such features would simply not work (for example, their menu options could be greyed out) if the module versions they depend on aren't there.
Your approach should work, but the risk I see is that you're giving yourself a lot more code to maintain if you need to make changes to the functionality.
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