feat/core runtime updates

[gknapp1]

Summary

First stacked PR from the #179 split. This isolates the non-thesis runtime work: Peregrine synonym expansion, portable configured-case paths, Docker run config support, and containerized deer/creep_timeseries_region execution.

These small changes are bundled to provide the context of the updates--getting the Deer module working with containerized executable environments.

Related issues

• Docker changes related to Separate Docker subprocess launcher from base suprocess launcher #126, but does not fully close.

Details

This PR extracts the runtime-focused changes that touch shared infrastructure and Deer execution behavior.

It adds portable configured-case handling by relativizing runtime-local paths during myna config and resolving them again during load. It also expands configured layer-range syntax into explicit layer lists at input-load time.

It extends MynaApp Docker execution so step configs can supply a YAML or JSON file of docker.containers.run(...) kwargs via --docker-config. The shared subprocess launch path was also cleaned up so sourced environments chain with &&, and Docker commands are invoked through bash -lc.

On top of that runtime plumbing, this PR adds Deer container support and updates creep_timeseries_region to stage and discover the case mesh more robustly before execution.

Impact

This changes shared workflow/runtime behavior and Deer execution behavior, so the impact is functional and cross-cutting but still bounded to well-defined extension points.

Risk level: Medium. The changes touch shared input loading and subprocess/Docker launch paths, but they are covered by focused regression tests and isolated to existing runtime hooks.

Architecture/docs: no update needed - this extends existing workflow path handling, Docker launch plumbing, and Deer app behavior without changing subsystem boundaries.

Testing strategy

Commit hooks passed during commit creation.

Covered by focused tests in CI-relevant areas:

• tests/test_load_input_paths.py
• tests/test_configure.py
• tests/test_app_argument_parsing.py
• tests/test_deer_creep_timeseries_region_app_behavior.py

Stack context:

• Base branch: origin/main
• PR branch: stack/core-runtime
• Stack position: 1 of 3

Checklist

• Architecture/docs impact considered. Updated ARCHITECTURE.md and/or
  developer docs where needed, or explained why not.