Simplify MCP tool surface

[rajeeja]

Summary

• Reduce the registered MCP surface from the flat implementation list to 11 front-door tools.
• Add tools/frontdoor.py with high-level dispatchers: run_analysis, plot_dataset, diagnose_endpoint, manage_session, get_status, and get_result.
• Keep low-level implementation functions available as Python APIs and internal workflow calls.
• Update slash-command prompts, capabilities output, README, tools docs, architecture docs, and workflow/HPC guidance to point at front doors instead of low-level verbs.

Visible MCP tools after this change

1. get_capabilities
2. analyze_dataset
3. run_analysis
4. plot_dataset
5. diagnose_endpoint
6. probe_path_access
7. run_workflow
8. resume_workflow
9. get_status
10. get_result
11. manage_session

Validation

• uv run pre-commit run --all-files
• uv run pytest tests/ --ignore=tests/test_remote_agent.py -q -> 293 passed
• uv run --extra hpc pytest tests/test_remote_agent.py tests/test_hpc_safety.py -q -> 44 passed
• uv run --extra docs sphinx-build -b html docs docs/_build/html -W --keep-going
• rm -rf dist && uv build && uvx twine check dist/*
• Live FastMCP registration smoke -> 11 visible tools listed above