Refactor and clean up reference variables

[sirbrillig]

This removes the multiple different ways used to track variable references and instead uses one.

This follows on the work done in #126/#128 and #120 and fixes some edge cases there. Notably, the sniff now treats a local assignment by reference (eg: $foo = &$bar;) as a declaration, not an initialization, since it doesn't really modify the value of anything, it effectively just creates an alias. That means that if the alias is unused, it should be reported as unused (which was already sort-of happening but it was a bit of a hack).

It also means that before we make such an alias, we should check and report if the variable is unused from a previous binding or assignment because after that point, it will effectively be a new variable.

The biggest change in this PR is probably that now every instance of an unused variable counts as a warning, rather than just the first. The reason for this is that if we do not report later instances, if the first instance is ignored (eg: by //phpcs:ignore), the later instances wouldn't be reported at all.