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Release v0.5.0: dynamic bounds, session persistence, calibrated quotas#6

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senseibelbi wants to merge 6 commits intomainfrom
release/v0.5.0
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Release v0.5.0: dynamic bounds, session persistence, calibrated quotas#6
senseibelbi wants to merge 6 commits intomainfrom
release/v0.5.0

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This PR releases PBPK MCP v0.5.0.

Included changes

  • Dynamic weight-scaled parameter bounds with allometric scaling
  • Cross-parameter consistency validation (13 organs)
  • Simulation persistence across restarts (Redis-backed registry + rehydration)
  • PBPK-05 load test validation calibrated to 0.25 MB/patient
  • Dev JWT warnings eliminated (secrets bumped to 32+ bytes)
  • Version bump to 0.5.0 across pyproject.toml, package, compose, env, and docs

Verification

  • Lint: passing
  • Runtime Contract: passing

Major changes:
- Dynamic weight-scaled parameter bounds with allometric scaling
- Cross-parameter consistency validation for 13 organs
- Simulation persistence across API container restarts via Redis-backed registry and startup rehydration
- PBPK-05 load test validation: memory estimator calibrated to 0.25 MB/patient from live rxode2 profiling
- Eliminated PyJWT InsecureKeyLengthWarning by lengthening all dev secrets to 32+ bytes
- Added population_load_test.py benchmarking script
- Added unit tests for startup rehydration and memory regression
- Fixed snapshot_store injection in JSON-RPC transport path

Test suite: 285 passed, 1 skipped
- Fix ruff lint errors (E402, UP031) in test files
- Bump .env.example SERVICE_VERSION to 0.5.0
- Add v0.5.0 section to CHANGELOG.md
- Remove deprecated MCP_MODEL_SEARCH_PATHS from docker-compose.celery.yml
- Remove duplicate summaryTransportRisk path in trust_surface.py
- Fix audit verify storage fallback to respect config default
- Regenerate contract artifacts to match current source tree
…ross-platform mismatch

The Runtime Contract CI job was failing because the committed
release_bundle_manifest.json included OECD_PBPK_guidelines.pdf,
which exists locally but is untracked and therefore absent on CI
runners. This caused a 198-byte deterministic-output mismatch.

- Add OECD_PBPK_guidelines.pdf to COPY_IGNORE_GLOBS
- Regenerate contract_manifest.json, release_bundle_manifest.json,
  and src/mcp_bridge/contract/artifacts.py
- Remove temporary CI debug upload step
Update README.md whats-new heading and SERVICE_VERSION table
entry from 0.4.4 to 0.5.0. Regenerate dependent manifests
and packaged artifacts module.
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