Fix for output of ADAPTIVE_PATH

[gtribello]

Description

This change ensures that when you output the newly fitted path that you get by running the ADAPTIVE_PATH method the output pdb file contains the same residue numbers, beta and occupancy values as the input path. The change to mapping/rt-adapt-alt-rmsd comes about becuase the residue numbers in the output are now correctly coppied from the input

Target release

I would like my code to appear in release 2.10

Type of contribution

• [x] 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

• [x] 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

• [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.

[gtribello]

I think this change is uncontroversial @GiovanniBussi. If you can accept the PR as soon as possible that would be great.

[GiovanniBussi]

OK for me! Is this to be fixed also in v2.9? Or is that already ok?

[GiovanniBussi]

And: the current PR is on master, maybe should be retargeted to 2.10

[gtribello]

@GiovanniBussi To retarget it on 2.10 do I just make a new branch off 2.10 and cherry-pick this commit onto it?

[GiovanniBussi]

@GiovanniBussi To retarget it on 2.10 do I just make a new branch off 2.10 and cherry-pick this commit onto it?

Yes

[gtribello]

Redone but based on 2.10