refactor(core): deprecate old fetch entities methods in favour of get_entities

[AlessandroPomponio]

Summary

This PR simplifies sample store entity retrieval by consolidating callers onto the newer get_entities() API, deprecating older fetch helpers, and updating affected tests and internal usages accordingly.

High-level Changes

• Replaced internal and caller usage of legacy entity fetch methods such as entityWithIdentifier() and entities_with_identifiers() with get_entities().
• Removed duplicated SQL-based retrieval logic from deprecated helper methods and turned those methods into thin compatibility wrappers that emit deprecation warnings.
• Updated related sample store and discovery space manager code paths to use the unified retrieval flow.
• Adjusted tests to validate the new calling pattern and explicitly assert deprecation warnings for legacy methods.

Impact

This change reduces duplicate retrieval code, standardizes entity loading behavior around a single API, and makes the deprecation path for old sample store access methods explicit. Existing deprecated methods still work for now, but downstream code should migrate to get_entities().

AI Disclosure

The code and this PR description were generated using IBM Bob (https://bob.ibm.com/) and were reviewed manually.