Adapt ESMValTool to new configuration

[schlunma]

Description

This PR adapt all parts of ESMValTool to the new configuration (see ESMValGroup/ESMValCore#2448).

• Related to New configuration file plan ESMValCore#2371
• Fixes Documentation build is broken #3762

Deprecation

Similar to the corresponding ESMValCore PR, this PR deprecates the command line option --config_file for esmvaltool data format/download/prepare. This option is scheduled for removal in version 2.14.0. Please use the option config_dir instead.

Example:

Old syntax:

esmvaltool data format --config_file=~/my/config/file.yml WOA

New syntax:

esmvaltool data format --config_dir=~/my/config/ WOA

See ESMValGroup/ESMValCore#2448 and ESMValGroup/ESMValCore#2371 for further details.

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