I'd go the route choroba stated, and wrap it into an early test in the test suite (eval to fetch).
Perform a significant number of tests against the version that is bundled with the module, and then perform the same extensive tests against the new version before installing it, as to ensure you don't break functionality of the module with a new version of the updated files during your install.
This way, by not doing it in Makefile.PL or something, if the fetch fails, or your unit tests don't pass on the new version of files, you can lean back on the existing bundled versions.
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