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Hey Snow,
Unfortunately, this is not really possible for the module dev's if they adhere to using all of the available XOOPS functions.
EG: All of the 'Preferences', 'Comments', 'Notifications', and Module / Block permissions are tied to functions (and tables) from the core.
Sure it takes some time to reset the options, etc... But what I think we need to push more for is for Module Devs to use the tools that GIGOE has put together for D2 & D3 (Duplicatible) Modules. All the sudden it only takes a couple of minutes to reset the permissions when everything you need to set is available from within the module admin section (Group & Block Permissions & positioning, Prefs, etc).
Unfortunately, there is still a real lack of clarity and standards for Module Development, made worse by the current Repository problems and lack of PHP5 support in legacy modules (which can usually be fixed in a matter of minutes if you know how) etc...
While it would be nice to have all of the data related to a module within the module tables, that would essentially require a much stricter (Development) standards set, would break most, if not all current modules, if introduced into the core, and would alleviate the benifits of having core functions for developers to 'Hook' into.
So while I understand the issue you raise, I think the resolution lies in providing all of the modules Options to be accessible from within the module as opposed to trying to move the Core data/functions into Module tables.
Thoughts?