Multiple updates to metatomic integration

[Luthaf]

Description

Fix #1337 and update the code to work with the latest releases and use the latest utilities.

The main change is added support for multiple variants of the same output in one model, i.e. having a single file that can produce any of features/soap, features/dihedral, features/my_custom_thing, and pick one at runtime.

Target release

I would like my code to appear in the next patch release for v2.10

Type of contribution

• [ ] changes to code or doc authored by PLUMED developers, or additions of code in the core or within the default modules
• [ ] changes to a module not authored by you
• [x] new module contribution or edit of a module authored by you

Copyright

• [ ] I agree to transfer the copyright of the code I have written to the PLUMED developers or to the author of the code I am modifying.

• [x] the module I added or modified contains a COPYRIGHT file with the correct license information. Code should be released under an open source license. I also used the command cd src && ./header.sh mymodulename in order to make sure the headers of the module are correct.

Tests

• [x] I added a new regtest or modified an existing regtest to validate my changes.
• [x] I verified that all regtests are passed successfully on GitHub Actions.

[Luthaf]

Can I update the Python version in CI from 3.9 to 3.10? 3.9 is EOL since October 2025.

[Iximiel]

Can I update the Python version in CI from 3.9 to 3.10? 3.9 is EOL since October 2025.

I would prefer to do that in an ad hoc PR @GiovanniBussi @gtribello maybe we should also move the requisites for the various pip packages in some explicit requirements file?

[Luthaf]

Sure, I can do the update in a separate PR.