Fix #94: resolve instance cross-references to typed Python objects instead of raw dicts

[apdavison]

Summary

Fixes #94. Library instances such as Accessibility.direct_virtual_open_access stored
properties like payment_models (and similarly channel, eligibility, form,
process, and equivalents on other classes) as raw {"@id": "..."} dicts rather than
as references to the typed Python objects they point to (e.g.
PaymentModelType.zero_cost_payment_model). This broke validate(), and caused a
KeyError in Collection.load() after a save/reload round trip, because the referenced
instance was never included in the saved collection.

Root cause

During code generation, the builder treated {"@id": "..."} values found in instance
data as opaque strings and emitted them verbatim, instead of resolving them to references
to the corresponding generated class attributes.

Fix

Resolve @id references to typed objects. Instance properties whose value is a
{"@id": "..."} dict (or a list of such dicts) that matches the @id of another loaded
instance are now emitted as references to that instance's generated Python attribute
(e.g. payment_models=[PaymentModelType.zero_cost_payment_model]) rather than as a
literal dict. References that don't resolve to a known instance (pre-existing dangling
@ids in the upstream data) fall back to the previous raw-dict behaviour.

Handle mutually-referencing classes. Resolving references this way exposed circular
import problems wherever two classes reference each other's instances (e.g.
ParcellationEntity and ParcellationEntityVersion in sands/atlas, v3/v4). The
generation of instance code was restructured so that such references no longer need to
be resolved at class-definition time: instances are first created with the properties
that don't create a cycle, and the cyclic ones are filled in afterwards, once every
class involved has been defined.

Test plan

• Added a regression test (pipeline/tests/test_regressions.py) reproducing the
  reported scenario: building a collection containing Accessibility instances,
  validating, saving, and reloading, and asserting that cross-referenced properties
  are typed objects rather than dicts.
• Full pytest -v pipeline/tests suite passes against the rebuilt package, including
  checks that mutually-referencing instances (e.g. ParcellationEntity /
  ParcellationEntityVersion) resolve to typed objects with no import errors.