(NOTE) Whether all this is even possible, or within my own skill level, I have no idea, but at least a preference for Special:ManageWiki/extensions seems like a good place to startI have no idea. Some of this will most definitely need community feedback for, so tagging #notice. However, I can't give a 100% guarantee, at least for me, that I'll actually be able to successfully implement all of this. Although, we can definitely try and start somewhere, and gradually implement some of the others in the longer-term, that I'll actually be able to successfully implement all of thisunless it is deemed impossible to achieve at the moment.
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### Module Improvements
#### Core
Special:ManageWiki/core could potentially be improved by maybe moving some of the primary settings, such as favicon, apple-touch-icon, logo, wordmark, default skin, and default mobile skin, etc... to Special:ManageWiki/core.
#### Extensions
One idea I have for this is to create a preference to be able to disable section tabs within Special:ManageWiki/extensions, with the exception of "Other" and "Skins", which would revert to the old behavior of Special:ManageWiki/extensions. The reason this would be a good idea is it would maybe allow easier discovery of extensions, by being able to search using the browser word search functions. Additionally, the creation of the sections never went through community feedback, as it was before SRE really started doing that. Whether this can even be done is yet to be seen, but it does seem like a good idea to attempt to do it. Furthermore, if the preference is not enabled, we should consider the redesign of the current sections for better discovery, as they currently for the most part use the sections in extension.json, which isn't always ideal, and it's hard to find some extensions.
#### Settings
Redesigning and reorganising the current sections of Special:ManageWiki/settings may be a good idea. We could also consider maybe pulling setting descriptions from the configuration description or descriptionmsg from extension/skin.json. Also, since Special:ManageWiki/settings, does support filtering by extensions or skins now at Special:ManageWiki/settings/<name>, we could maybe add a dropdown box or something above the form with options for each extension for easier filtering and visibility of each enabled extension's/skin's available settings, with the addition of MediaWiki core and all global extensions/skins as options as well.
#### Permissions
We could potentially improve Special:ManageWiki/permissions by maybe making it possible to add at least one configuration variable to the main part of Special:ManageWiki/permissions, before entering into group permission modification. We could add the ability to create custom rights within the `$wgAvailableRights` configuration, which of course would need vetted to adhere to the disallowed rights, etc. But doing this would potentially allow adding one of the most requested configuration variables to ManageWiki, `$wgRestrictionLevels`.
#### Namespaces
At least one improvement I can think of for Special:ManageWiki/namespaces can be made. We could potentially make it possible to add multiple values for `$wgNamespaceProtection`, as that config supports an array for multiple values as well. Some extensions even set multiple by default, but because of the fact we don't support them, ManageWiki only supports one, and therefore, only one is in the install step of ManageWikiExtensions. An example of this is StructuredNavigation, for the "Navigation" namespace. The extension has two namespace protection permissions, !!structurednav-edit!! and !!structurednav-create!!, but since ManageWiki only supports one, it only sets !!structurednav-edit!! in the extension install step.
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### Global Improvements
#### User Experience
We could potentially improve the overall flow of the extension, by using heavy JavaScript, to make the user experience better, and allow to continue on modifying the main form after selection of a group or namespace in their respective modules, interactively with JavaScript, so virtually it would not need to reload.
#### Discovery
We should consider further improvement and discovery of ManageWiki as a whole, to make it easier to use, provide better documentation, and make it more understandable and easy to use for less technical-oriented users. One idea could be a complete rewrite of the entire extension (or creation of a new module), which would essentially create a step-by-step wizard, either complete deprecation of the current modules, or a whole new module, which you could use to find extensions you want to enable, enable extensions, continue to the next step, manage namespaces, continue on to management of permissions and settings for the extension setup, with some sort for wizard or something else for core stuff management.
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### New Additions
#### Supporting Hooks
We could potentially consider supporting some basic hooks in ManageWiki, potentially by creating a new "hook" type for Special:ManageWiki/settings, which would be able to modify hook output, within ManageWiki. Of course, by doing this, we would definitely need some sort of validation/sanitisation for user input within ManageWiki.
#### Better Validation of Configuration Variables
We should consider maybe something like a new ManageWikiValidation helper class or something to support better validation for numerous configs in both Special:ManageWiki/settings and Special:ManageWiki/namespaces. This would validate stuff like usage of !!https!! where required, to prevent user confusion, or CSP errors which would sometimes be given, if it is done incorrectly, and would immediately give the user an option to correct their mistake, and not save the setting otherwise.