Also, fix for notifications throttle delay value

This big commit ties the knot with the named _routes_ by providing
concrete server (i.e. handlers) implementations.

This big commit adds a separate module hierarchy for Servant named
routes (see https://www.tweag.io/blog/2022-02-24-named-routes/ ) which
will make working with servant endpoints more pleasant (especially when
it comes to emitted errors).

This still doesn't do anything to wire the routes to the concrete
handlers.

This commit moves away from generic-derive JSON istances for `NodeType`,
as we know that the frontend will be relying on this in the GraphQL API,
and we don't want them to silently break the frontend during
refactoring.

It was only for test for now.

Tests were written with a very flat module hierarchy which made them
a bit confusing to navigate. This commit moves everything under a common
`Test.*` hierarchy.

This commit fixes the `testWithQueryFrontend` test, which was broken by

6bc41d73

However, this was followed by a frontend fix, which was modified to deal
with the next format:

purescript-gargantext!374 (diffs)

Therefore, it's fine to fix the test here.

This commits changes the `PhyloData` data structure to
include a proper `GraphData` in the `pd_data` field. The
`GraphData` is almost complete, but the `objects` field needs
to be further refined from a generic JSON `Value` to proper
Haskell types.