Complete MolSysSuite policy adoption on Python 3.11–3.13

[LMMV]

TopoMT now declares the shared Python >=3.11,<3.14 range, uses Ruff target py311, tests the 3.11–3.13 matrix, and excludes synchronized root guides in 7ecdc43. This implements the metadata and vendored-guide part of uibcdf/molsyssuite#6 and uibcdf/molsyssuite#12.

The first CI run exposed remaining local adoption work instead of a product regression:

• the test environment omits the direct argdigest dependency, so 3.11 and 3.12 fail during import;
• released MolSysMT packages are not yet available for Python 3.13 in the configured conda channels;
• the current Ruff job checks only selected critical rules; the complete shared ruff check . and ruff format --check . gates still require an isolated mechanical cleanup (currently 344 lint findings and 218 files needing format under the repository settings).

Acceptance criteria:

• make all declared direct test dependencies available in CI;
• define and validate the Python 3.13 dependency source without weakening the 3.11–3.13 contract;
• make the shared Ruff lint and format commands green in a dedicated mechanical change;
• call uibcdf/molsyssuite/.github/workflows/check-python-repository.yaml@policy-v1.1.4;
• confirm the full Python matrix and MolSysSuite policy workflow are green.

This incubating-component work does not block the wave-1 stabilization subset, but it remains required before TopoMT claims policy adoption.

[LMMV]

MolSysSuite adoption checkpoint (2026-09-22): the caller now pins the current immutable release policy-v1.4.5 in commit 8ff065a, superseding the historical policy-v1.1.4 acceptance-text target. Hosted run 35723875941 reached the current policy but failed Check Python lint and imports; GH Run Receptor preserved the failure, and native logs measured 603 Ruff findings under the repository configuration. The pin is current, but adoption is not green. This issue remains the local migration owner and is linked from uibcdf/molsyssuite#34.