restructure codebase

[clemsgrs]

Summary

This PR continues the package-cleanup effort by splitting slide2vec.inference into workflow-scoped runtime modules while preserving behavior and current public API usage.

Major steps shipped

1. Refactor inference into runtime workflow modules

• Added slide2vec.runtime package with:
  • batching.py
  • hierarchical.py
  • progress_bridge.py
  • serialization.py
  • types.py
• Rewired slide2vec.inference to consume these helpers.

2. Extract distributed inference helpers into runtime module

• Added slide2vec.runtime.distributed for:
  • torchrun orchestration/log capture/progress streaming
  • distributed coordination-dir lifecycle
  • rank assignment
  • shard merge/load helpers
• Kept compatibility shims in slide2vec.inference for existing monkeypatch/test patterns.

3. Extract pipeline artifact persistence from inference

• Added slide2vec.runtime.persistence for:
  • artifact discovery/loading
  • process-list status updates after embedding
• Reduced orchestration clutter in slide2vec.inference.

4. Extract tiling/embedding helper domains + architecture boundaries

• Added slide2vec.runtime.tiling for pure tiling config/backend/archive/coordinate helpers.
• Added slide2vec.runtime.embedding for metadata + artifact writer helpers.
• Added runtime import-boundary guardrail to prevent runtime modules from depending on CLI/package facade.

5. Declutter root package module surface

• Moved internal root modules to clearer homes:
  • slide2vec/runtime_types.py → slide2vec/runtime/types.py (LoadedModel)
  • slide2vec/model_settings.py → slide2vec/runtime/model_settings.py
  • slide2vec/registry.py → slide2vec/runtime/registry.py
  • slide2vec/resources.py → slide2vec/configs/resources.py
• Updated internal and test imports accordingly.
• Added a guardrail test that enforces a curated, minimal set of root-level package modules.

6. Trim secondary tests to keep suite focused

• Removed low-signal/secondary tests:
  • tests/test_docs.py
  • tests/test_packaging_metadata.py
  • tests/test_batch_collator_timing.py
  • tests/test_output_consistency.py
• Kept core regression, model, progress, registry, tile-store, and architecture suites.

Guardrails + docs

• Added/extended architecture guardrail test: tests/test_architecture_runtime_split.py
• Updated docs log in docs/documentation.md.

Outcomes

• slide2vec.inference.py reduced from ~3753 lines to ~981 lines.
• Root package Python files are now curated to a smaller, intentional set.
• Runtime concerns are split into focused modules by domain.
• Test suite is sharper and more focused on core behaviors.