Additionally to this I want an ability to flag addons disabled without removing files, intentionally. Each addon would get to declare whether this is supported - I don't want coders hacking stuff up, or 3rd party addon makers, to have to make addons this robust - but I want all the bundled addons to support it.

So before checking tables etc, addon_installed would also check simple get_value calls to see if there's a flag to say the addon is disabled.

All done, except..

"admin_addons should be able to detect corrupt addons and allow either repairing them (extract missing files and install modules and blocks), reinstalling, or deleting them."

Instead I've made the upgrader a bit nicer, and error messages about addon/block/module issues will now point to both the upgrader and admin_addons, with explanations of what circumstances to use each. I think this is a lot cleaner, as the upgrader already had the role of Composr's repair tool.

"The integrity checker should get a lot smarter. It should be able to detect addons that are not properly installed and provide groups of files to delete under a single checkbox."

I didn't see a good reason to do this. But I have tuned the messaging, it's pretty clear how to deal with a partly-installed addon now.

"A lot of work needs doing in the integrity checker to make a better API, and it should be unit tested."

The upgrader code has been improved a lot. It makes use of a lot more shared code with the rest of Composr. I haven't specifically unit tested though as that would be challenging and quite messy.

"As a general test make a quick Composr site with no optional addons installed, then put ALL the files back and make sure nothing crashes. Then make sure the upgrader can cleanup the situation either by repairing addons or by deleting files."

I haven't done this extensive testing, but the automated testing for checking addon checks is pretty exhaustive, and I've done some testing (intentionally breaking the meta DB, and removing a registry hook - confirming menus update). If there are issues it will come up in automated error emails.

"Additionally to this I want an ability to flag addons disabled without removing files, intentionally. Each addon would get to declare whether this is supported - I don't want coders hacking stuff up, or 3rd party addon makers, to have to make addons this robust - but I want all the bundled addons to support it."

I haven't done the white-listing, as I think that's unnecessary. I've simply documented in the Code Book that not all addons will support it.
The ability to disable addons without removing files is a great addition to Composr, something I've wanted for a long time. It will potentially allow Demonstratr sites to run with different addon sets, although there's no UI for defining what addons are disabled right now.

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I also made it so addons check their dependencies at run-time.