MAINT: Formalizing the `con` format

[HaoZeke]

In general the con file format is great. However, there is a dependence on the Atom ID which is currently implicit, it determines the ordering of components, and therefore the order of counts and masses in the header as well.

There are a few options here:

• Store Atomic ID in the Matter object explicitly, and use its ordering (current behavior)
  • This is implicitly enforced but it is a bit awkward
  • Would make it easier to ensure consistency wrt LAMMPS if this is explicit
• Choose a default order, e.g. say the atomic mass order
  • Programmatically easier, but then mapping to say, LAMMPS might need more work

Basically for the first case, Matter needs some rework, so this is part of #170.

[HaoZeke]

Atom ID is now part of the Matter object. Documentation needed to close this out.