Use trips as primary unit for filtering, cascade changes upwards, and remove nonexistent association

[brookeangel]

Addresses: #6

This PR contains several breaking changes to existing behaviors:

• The graph is now undirected, so changes "cascade upwards" - e.g. if I remove a route and an agency is unreferenced, it will now be removed
• We now use trips as the "atomic" unit for filtering - this means if I filter to a Stop A, we will first generate the list of all trips that use Stop A, then we will filter to those trips & all their dependencies reference. (So, we won't just end up with Stop A in the filtered result, but also any other stops the trip visits). This mimics the intended behavior of partridge: Bug fix: Preserve complete trips by resolving trip_ids from filters remix/partridge#66
• A nonexistent association between stops & booking_rules is removed. See: https://gtfs.org/documentation/schedule/reference/#booking_rulestxt

See issue and tests for examples.

[davidmh]

How come we avoid mutating here but we do mutate in prune!?

If useful, could we leave it as a comment in the code?

[brookeangel]

Yeah sorry, that is awkward! Let me see if I can better arrange, or if not, leave a comment

[davidmh]

🚀