Separate all UI visual effects theming from module (move to themes)

Problem/Motivation

(why the issue was filed, steps to reproduce the problem, etc.)
For my theme I had to exceed use of navigate-custom.css (well.. i did- there may be a way to do, what I did via the navigate-custom.css) but i hacked the module/javascript to override the javascript opacity properties to remove the transparent/overlay affect.

It seems I also had some other issues where navigate core theme was not easily overriden by navigate-custom.css, that inspired me to create a navigate_mint theme folder for my theme, to which I link all themes that I am using/testing (as it is a major concern to me any theme/changes be compatible with navigate). Then (I think) I stripped the css & images out of the module just to confirm i could get the look I wanted... all very bad hacks which are not maintainable with an update of the module.
Navigate is SO great.. that even if I have to manually & update/reset my theme.. it is worth it!

Theme screenshot attached- I hope you like my take on the navigate switch.. as Navigate can put the entire world of a Drupal site within easy access!

Please let me know if you want a copy of the files. I will be happy to provide it.
It still needs some tweaks but I am happy with it.

Proposed resolution

(description of the proposed solution, the rationale behind it, and workarounds for people who cannot use the patch)
So.. an GREAT enhancement/new feature, would (for folks like me) be to separate the theming with a mini theme for the all/themes folder; for easy updates, skinning a variety of themes for multi-sites & copying to new sites.
if the javascript opacity must be in the js/core files
- a User Interface to adjust properties?
- several variations and a way to select/enable (rename?) the desired variation with user preferred javascript/properties? Once renamed the selected variation would not be overwritten by updates, and the user would manually enable/rename the updated version after running update?

Remaining tasks

(reviews needed, tests to be written or run, documentation to be written, etc.)

User interface changes

(new or changed features/functionality in the user interface, modules added or removed, changes to URL paths, changes to user interface text)

API changes

(API changes/additions that would affect module, install profile, and theme developers, including examples of before/after code if appropriate)

Related Issues

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Original report by [username]

// Text of original report here.
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