The new v3 applets don't use it, and eventually all applets will
use the new formats only.
This prepares the code for this, and moves trust, id_cache, and
root_fd to apk_ctx which is enough for v3 applets at this time.
The generic code is made to not initialize apk_database if it's
not needed.
This greatly helps with memory management on applications that
may want to daemonize and open/close database several times.
Also the lifetime and "owner" of memory for all data is now
explicitly bound to owning struct apk_database, which might
be helpful when writing language bindings. As side effect, the
interned "atoms" are unique only within what apk_database, so
comparing packages from different apk_database may not work
as expected.
Fixes#10697
Timo Teräs