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Remove re-writing config.toml file on configuration reload

Tomasz Maczukin requested to merge remove-configuration-rewriting-in-run-command into main

What does this MR do?

Removes configuration file saving on reload.

Why was this MR needed?

Saving reloaded configuration was added to automatically handle rewriting configuration fields that are going to be renamed (which have a deprecated old key and a new key that is preferred). This mechanism is however creating more troubles than it fixes. For now it will be better to remove the save call and think later about a better approach to make user's transition between deprecated->new configuration fields easier.

What's the best way to test this MR?

What are the relevant issue numbers?

Edited by Tomasz Maczukin

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