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Remove additional public tools from private ToolHandles in ID configs

Merged Thomas Strebler requested to merge tstreble/athena:IDToolPublicCA into 23.0

Following !61296 (merged), some public tools are now private and can be updated consequently in the CA configs. Also includes autopep8 formatting as separate commit. Connected to ATLASRECTS-7597

Run 3 and Run 4 outputs unchanged.

FYI @wlampl @jmasik

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