Reduce direct use of numerical part id (doc, samples)

[pkreissl]

Part of #4029

Description of changes:

• make vs_auto_relate_to() take ParticleHandle, not just particle id
• remove particle id from doc and samples wherever possible
• improve checking of arguments for VS and bonds (e.g. prevent adding the same bond twice by calling add_bond() with a particle id and calling it again with the corresponding particle handle)

There are still some places, especially in the espressomd.observables, where for now particle ids cannot be omitted, such as ParticlePositions.

[KaiSzuttor]

👍 really good stuff

[KaiSzuttor]

none of your business but this variable name is not too descriptive and the underscore is not pep8... just if your over-motivated :)

[pkreissl]

I agree, the current variable names in this part of the interface are not as I would like them to be. However, this is true for all member variables of the ParticleHandle class. I think the idea here is to mirror the core variable but adding a prefixed underscore to not have the variables being exactly the same. I think @RudolfWeeber commented in some PR (that I can't find just know), that he would like to have distinct names for the variables in core and interface respectively. If I am wrong here, sure I can quickly go over the class and "pepify" it a bit.