Refactor: move config reads out of dataclasses and algorithmic functions

[nicoloesch]

Problem

OmopGraphConfig.get_config() (and OmopEmbConfig.get_config(), see associated issue) are called deep inside pure functions and dataclass field defaults rather than at system boundaries. This couples algorithmic code to the file-based config system, makes unit testing require a real config file, and hides I/O inside what appears to be a data construction or arithmetic call.

Specific locations:

src/omop_graph/reasoning/grounding.py:78

max_depth: int = field(
    default_factory=lambda: OmopGraphConfig.get_config().max_depth
)

A frozen dataclass reads config on every instantiation where max_depth is not supplied. Any test that constructs GroundingConstraints without max_depth (e.g. via annotate_text) fails without a config file.

src/omop_graph/graph/paths.py:259, 472, 784

cfg = OmopGraphConfig.get_config()
if max_depth is None:
    max_depth = cfg.max_depth

Config is read inline inside graph-traversal functions when optional parameters are absent. A caller that passes explicit values never touches config; one that omits them triggers a file read buried inside an algorithmic function.

src/omop_graph/graph/kg.py:194

cfg = OmopEmbConfig.get_config()

Config from a sibling package is read during KG initialisation, coupling KG construction to omop-emb's config file presence.

Root cause

Config reads are scattered across the call stack rather than consolidated at entry points (CLI commands, service constructors, or test fixtures). Pure functions and data classes should receive explicit values; only boundary code (CLI, factory functions, integration test setup) should call get_config().

Proposed direction

1. Change GroundingConstraints.max_depth to default=6 (the same literal as the Pydantic field default in OmopGraphConfig). Callers that want to honour user config read it explicitly and pass it in.
2. Remove inline get_config() calls from paths.py functions. Callers that omit max_depth/max_paths and want config-driven defaults should resolve them before calling; alternatively, expose a thin wrapper at the service layer that does the config read once.
3. Remove the OmopEmbConfig.get_config() call from kg.py. Pass the required config values as constructor parameters so the KG remains independent of the omop-emb config file.