Schema Version reset to -1 when update.module cache is cleared

This is probably related to #706608: system_update_files_database() called from update_get_projects() breaks system table on cache clear since status is also set to 0. This also happened in the tests but has been fixed there by running cron as the installer does.

Have any idea how they got reset?

That's equivalent to removing it entirely. I'm sure it needs to be cleared but let's see what happens if you don't.

- *Something* seems to be causing this, right now, it's update.module but removing the clear_cache_all() is imho not a proper fix. This could as well happen in a contrib module and then it will be a lot harder to debug. How can a clear_cache_all() have any effect on the {system} table? That shouldn't be possible...

- Once fixed, this imho needs a test case to reproduce the breaking behavior to make sure that it doesn't happen again.

I'll try to go over this with an debugger...

Yeah it's not a proper fix, I just want to see if that's actually what's causing it.

Also, the presence of that cache_clear_all() is troubling in itself, as far as I know dww wrote a bunch of helper functions to avoid using cache_set() cache_get() and cache_clear_all() on {cache_update}, however it's now in system_flush_all_caches() and explicitly cleared in update.php, so something's dodgy there anyway. Changing component.

This has to be the same bug as #706608: system_update_files_database() called from update_get_projects() breaks system table on cache clear, so marking as duplicate. See you over there.