After some browsing through the code and the database it looks like there are no tables linking to the id column of the capabilities table? That table is mostly used to produce the UI lists for setting the role permissions etc.? Also, if the capability is missing from that table, Moodle says that it's missing completely. When, in our case, as the role_capabilities looks to be in order, things are working nicely by just setting Moodle to ignore the error messages. Updating the roles for the core capabilities is impossible though, so obviously I need to fix this...
I'm now testing (on a dev copy) just adding the missing standard capabilities to the capabilities table. So far looks ok, but I'm now stuck in a myriad of not-well-formed-xml, probably my own customization mistakes...
Roles and permissions
How to add missing capabilities?
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