fix(research): mount read-only Obsidian tools instead of rag for vault KBs

[szzhoujiarui]

Description

When a connected Obsidian vault is selected as the knowledge base, the deep-research pipeline auto-mounts the rag tool even though the vault has no index, producing spurious warnings and misleading evidence. This PR makes ResearchPipeline vault-aware:

• Resolve KB metadata at construction (resolve_kb_metadata) and record _is_obsidian_kb / _vault_path (pure read, no RAG usage audit).
• Suppress the rag auto-mount for Obsidian KBs (has_kb=False) and expose the three read-only Obsidian tools obsidian_search / obsidian_read / obsidian_list in the research block loop.
• Keep Obsidian type detection independent from vault_path availability, so malformed metadata never falls back to index-backed rag; read tools are mounted only when a trusted path exists.
• Inject _vault_path server-side in _augment_tool_kwargs, overwriting any model-supplied value so the path cannot be forged to read outside the vault.
• Add the three tools to CITABLE_TOOLS so their evidence is summarised, recorded by the CitationManager, and reaches Phase 4 reporting.
• Preserve each tool's real citation locator (query, note, or folder), using / for a vault-root listing.
• Render an Obsidian-specific system note (en/zh) instructing read-only vault retrieval instead of rag.

Indexed KBs, no-KB, and unresolvable references keep their existing behaviour.

Related Issues

• Closes ResearchPipeline mounts rag tool for Obsidian KBs, producing spurious warnings #752

Module(s) Affected

• agents
• api
• config
• core
• knowledge
• logging
• services
• tools
• utils
• web (Frontend)
• docs (Documentation)
• scripts
• tests
• Other: ...

Checklist

• I have read and followed the contribution guidelines.
• My code follows the project's coding standards.
• I have run pre-commit run --all-files and fixed any issues.
• I have added relevant tests for my changes.
• I have updated the documentation (if necessary).
• My changes do not introduce any new security vulnerabilities.

Additional Notes

• 23 targeted tests in tests/agents/research/test_research_obsidian_tools.py cover metadata resolution, tool-composition matrix, vault-path injection/forging, real citation locators, and system-note selection.
• The targeted ResearchPipeline and Obsidian capability suites pass: 52 passed.
• Full backend suite from the initial implementation run: 3527 passed; 24 pre-existing failures in MCP/partners tests (reproduced on clean dev baseline, unrelated to this change).
• pre-commit run --all-files was not executed in this environment; the modified files pass ruff check, ruff format --check, and git diff --check locally.