UpdateMembership.php and other scripts don't survive upgrade

I have seen numerous sites where UpdateMembership doesn't work because the edited & renamed php scripts are deleted on upgrade and replaced by UpgradeMembership.php.txt.

I think we need to bring all config options OUT of the scripts in the bin directory. In the case of the UpdateMembership this may be already done but not renamed (I'm not sure if the absence of a reminder template for a given membership type means no e-mails go out - if so then it just needs to be renamed to .php not .php.txt when it ships as the from e-mail address has been set now). But there is also the pledge update & the waitlist update. Pledge update needs the option to determine whether reminders go out.

If this is going to take more than whatever amount you just suck up give me an estimate & I'll see if we can launch for Make-it-Happen