Fix plugin deprecations

Problem/Motivation

Plugins should be deprecated in the constructor and not the main section of the class. This is because discovery and instantiation can result in triggering unwanted deprecations.

Steps to reproduce

See tests runs on #3252386: Use PHP attributes instead of doctrine annotations where all plugins have been reflected on for discovery.

Proposed resolution

Move deprecation to constructor,

Remaining tasks

User interface changes

None

API changes

None

Data model changes

None

Release notes snippet

N/a