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Runtime settings were handed back to pydantic-settings as init settings,
which rank below the config file and the environment. Any key already
present in EOS.config.json or in the environment silently discarded the
update, so a bulk PUT /v1/config returned 200 without applying anything,
while the granular PUT /v1/config/{path} endpoint kept working.
Add a dedicated runtime settings source ranked directly below the command
line arguments and record granular updates there as well, so both
endpoints share one store that survives re-evaluation of the settings
sources. Environment variables keep precedence over the config file for
all keys that were not set at runtime.
Also repairs revert_settings() and update(), which passed their data
through the same init settings.
Closes #1303