I think the biggest thing is to not get too many authors updating files. This way if something breaks and one of them authors is no longer playing/updating it won't end up dead.
I know all the intentions are good but if theres a dozen people working on a project then its bound to run into some issues if someone did something that broke code and is no longer available.
I would say release your modified files as addons/optional as that way the default installation is always maintained by the updater.
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