Mklib deprecation warning for "core/Atoms.h"

[Iximiel]

Description

This should address the missing "core/Atoms.h" in the nest, more precisely it will only state that the header is deprecated, and then make proceed the compilation until there is a failure on an Atoms method that does not exists anymore, this may guide to update easier some error in the nest.

I also patched the template cv, so that now it can compiled as it is generated by plumed newcv

Target release

I would like my code to appear in release 2.10

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
• [ ] 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.

• [ ] 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

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

[Iximiel]

I also patched the template cv, so that now it can compiled as it is generated by plumed newcv

I removed this, since the modification break the compile chain