`std::optional` instead of `-1` indices

[no-lex]

Using -1 for an invalid index is not very safe and also not necessary due to the existence of std::optional. With std::optional it should be possible to at least use size_t indices, the appropriate type for the indices of e.g. a vector, if not std::optional<std::vector<>::iterator>. Many parts of the codebase involve a data structure containing integral indices referring to another data structure, and while this is not good design, moving to std::optional would be a step in the right direction.

[Duskhorn]

Do you mind if I start tackling this?

[no-lex]

of course not