LibOverride: Tweak RNA 'need resync' detection code.

* Assert about source ID of an overridden pointer property not being a
liboverride was not necessary, just skip in that case.
* Tag actual 'real' ID owner for resync, and not (potentially) an embedded one.

LibOverride: better handling of the "no override of bones' shapes" case.

Also avoid overriding collections of bone shape objects, if possible.

LibOverride: protect better against using on complex inter-dependency cases.

Do not allow 3DView operator to run on the liboverride of an
instantiating Empty object. And tweak behavior in the Outliner
operations too.

Related to T94226.

Note that this remains fairly exotic, bad idea not recommended cases,
such complex inter-dependencies between different libraries inside a
same liboverride hierarchy is just not possible to handle properly.

Cleanup: Remove debug print.

Fix (unreported) potential bug in collections parenting update code.

Own mistake in rB2ef192a55b2c. Did not seem to have any visible effect
though...

Cleanup: Use `LISTBASE_FOREACH_` macros.

Fix T93799: Outliner: Remaping objects could result in duplicates in a collection.

Fix is similar to how CollectionObject with NULL object pointers are handled.

Using one of the 'free' pad bytes in Object_Runtime struct instead of a
gset (or other external way to detect object duplicates), as this is
several times faster.

NOTE: This makes remapping slightly slower again (adds 10 extra seconds
to file case in T94059).

General improvements of remapping time complexity, especially when
remapping a lot of IDs at once, is a separate topic currently
investigated in D13615.

Fix part of T93799: Outliner: Remap Users crash (for `ID Type` `Object`).

This commit fixes the crash itself, however this can still lead to a
same collection 'owning' the same object several time.

Issue here was a bad assumption in layer resync code, that would lead to
removing valid objects from the viewlayer's `object_bases_hash` in
`BKE_layer_collection_sync`, when deleting no-more-used bases, in case
of bases duplicate.

Fix T93757: Do not force-instantiate indrectly linked objects in linking case.

Fix T93839: Copy/Paste of empty instantiating a collection.

Do not also instantiate a collection in the view layer, if it is already
instantiated through an empty object.