fix(knowledge): harden GraphRAG model and embedding compatibility

[Lan-zk]

Description

Fix the GraphRAG compatibility gaps described in #745.

• Preserve the selected DeepTutor chat provider and use the same provider-specific request options in compatibility probes and real indexing.
• Support native structured output where available, with a schema-in-prompt fallback and strict local validation for compatible custom endpoints.
• Normalize complete /embeddings operation URLs only in GraphRAG settings, preventing duplicated /embeddings/embeddings paths.
• Forward embedding dimensions and custom headers consistently, and reject transports GraphRAG cannot use safely.
• Run completion and embedding preflights before incremental updates write existing knowledge-base settings or input files.
• Surface stable, secret-free completion and embedding errors while keeping tracebacks in server logs.

Compatibility

• Existing GraphRAG index schemas and ready indexes are not changed or rebuilt.
• Stored global chat and embedding profiles are not rewritten.
• Other RAG engines retain their existing endpoint behavior.

Related Issues

• Closes [Bug]: GraphRAG request configuration diverges from DeepTutor chat and embedding profiles #745
• Related to [Bug]: GraphRAG 3.1.1 indexing is blocked by uvloop and invalid generated settings #695
• Related to SiliconFlow Embedding API 不兼容（HTTP 400） #651

Module(s) Affected

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

Validation

• Changed-file pre-commit hooks passed: Ruff, Ruff format, Prettier, detect-secrets, Bandit, and MyPy.
• 102 focused GraphRAG/logging tests passed; the three router import cases used a minimal test configuration.
• pytest tests/services/embedding: 104 passed.
• npm run test:node: 369 passed.
• npm run lint: 0 errors; 60 existing repository warnings.
• npm run build: passed.
• A complete re-index of an existing GraphRAG knowledge base succeeded with the patched DeepTutor 1.5.7 build.

Repository-wide pre-commit run --all-files still encounters unrelated baseline Prettier drift and the existing Bandit B108 finding in deeptutor/services/cli_apps/runner.py; those files are not changed by this PR.

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. See the baseline note above; all hooks pass on the changed files.
• I have added relevant tests for my changes.
• I have updated the documentation (not required for this internal compatibility fix).
• My changes do not introduce any new security vulnerabilities.