Resolve global Ruff findings after phenotype workflow sprint

Current state

ruff check acp_agent core mcp_server scripts tests reports 13 findings. Targeted Ruff checks for the phenotype workflow and companion R-client compatibility cleanup pass; this issue tracks the remaining repository-wide debt.

StudyAgent findings (inspect before removal)

acp_agent/study_agent_acp/agent.py contains earlier definitions that Ruff reports as redefined by later implementations:

• __init__ at lines 76 and 511
• list_tools at lines 504 and 1421
• call_tool at lines 507 and 1434
• unused local name at line 1336

The earlier methods appear to be obsolete stubs or shadowed implementations. Remove or reconcile them only after checking the class layout and ACP behavior; do not mechanically refactor the orchestration class. Run focused ACP routing, server, and phenotype tests afterward.

Other low-risk findings

• unused local name in acp_agent/study_agent_acp/phenotype_recommendation_utils.py
• unused allowed_set in core/study_agent_core/tools.py
• unused imports in tests/test_acp_cohort_methods_route.py and tests/test_mcp_phenotype_summary.py
• mid-file imports in tests/test_cohort_methods_spec_validation.py

Suggested completion checks

1. Run focused tests for every affected behavior, particularly ACP server/routing and phenotype recommendation tests when editing StudyAgent.
2. Run ruff check acp_agent core mcp_server scripts tests.
3. Run git diff --check.
4. Run the normal Python gate, uv run --extra dev doit test_all; separately report any unrelated existing failures rather than masking them.

Start by running ruff check acp_agent core mcp_server scripts tests and inspect the duplicate definitions in acp_agent/study_agent_acp/agent.py before changing them. Review the other listed files and run the focused ACP, phenotype, and affected tests. Done means the findings are resolved, the focused tests pass, git diff --check is clean, and uv run --extra dev doit test_all has been run with unrelated failures reported.