Add POST /simulations/runs listing endpoint + convergence plan

[jcschaff]

Summary

Implements the simulation-runs listing endpoint (backend, full persist + query) from docs/simulation-runs-api-plan.md, and adds a sequenced plan for converging the duplicate run-execution paths.

POST /simulations/runs (new)

• Persistence — SimulationRunRecord in a new BiosimSimulationRuns collection, written one-per-(submission × simulator) on POST /simulations/run at status=CREATED, then updated to SUCCEEDED/FAILED by SimulationRunWorkflow via a new update_run_status_activity. Internal processing/success/failure maps to the frontend's CREATED/SUCCEEDED/FAILED.
• Query — owner-scope (type: all|user + user email), pagination, sorting, filtering. Returns { runs: SimulationRun[], pagination: { page, perPage, _total } }. Filter ids are allowlisted (also blocks arbitrary-field injection).
• Plumbing — SimulationRunDatabaseService (+ Mongo impl); DI getter wired via a lazy import to avoid the simulations → dependencies import cycle; new activity registered in worker_main.py and the test worker fixture.

Test-isolation fix

The shared database_service_mongo fixture never cleaned BiosimSims on teardown, so the real-network test_sim_workflow leaked a SUCCEEDED record that gave later tests a spurious cache hit (failing integration_local in the full suite). It now cleans up on teardown, matching its sibling omex_database_service_mongo.

Convergence plan (docs/simulation-runs-convergence-plan.md)

There are currently two implementations of "run one sim on biosimulations.org" (the verify path's OmexSimWorkflow + monolithic activity, and this path's split submit/poll activities). The doc lays out four independently-shippable PRs to converge them: re-expose cache_buster, enrich BiosimSimulationRun parsing, reuse OmexSimWorkflow as the single per-run unit, and normalize SimulationRunRecord to FK into BiosimulatorWorkflowRun with a join-backed listing.

Known limitations (documented)

• Deferred fields (cpus, memory, maxTime, envVars, purpose, runtime, projectSize, resultsSize) default to 0/[] — the platform doesn't capture them yet (PR1 in the convergence plan sources them).
• No real auth — owner-scoping trusts the supplied email.
• Frontend follow-up: wire frontend/app/pages/simulations/index.vue (currently on mock data) to this endpoint.

Testing

• ruff clean; mypy --strict clean (biosim_server + tests).
• New tests/simulations/test_runs_query.py (query-translation unit tests, Mongo-backed service tests, endpoint tests) + end-to-end assertions in tests/integration_local/test_simulations_run.py — all pass.
• Full poetry run pytest -m "not integration": 74 passed, 1 failed. The single failure is the pre-existing test_slurm_service (UnboundLocalError, needs SSH creds) — environmental, unrelated to this change.

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