refactor: remove public answer_with_citations tool

[eunaverse]

Summary

• remove answer_with_citations from the public MCP tool surface
• keep demo, smoke, eval, and E2E answer coverage on direct CitationAnswerService calls
• align README, maintained architecture, ADRs, and harness docs with the smaller public surface while preserving sync_all and search_documents as public tools

Review notes

• public tool removal is covered by contract/composition tests instead of a live MCP answer call
• internal answer coverage remains in local demo/smoke/eval paths and retained E2E flows
• final fresh five-reviewer subagent pass reported no actionable findings

Verification

• uv run pytest -q tests/api/test_tools_contract.py tests/contracts/test_public_mcp_contracts.py tests/test_app_composition.py tests/e2e/test_contextwiki_flow.py tests/e2e/test_phase_b_connectors_flow.py tests/e2e/test_obsidian_connector_flow.py tests/scripts/test_live_query_smoke.py tests/scripts/test_demo_public_flow.py
• python -m compileall api core environments fetching indexing search storage main.py scripts evals
• ./scripts/verify_functional_e2e.sh
• git diff --check

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