chore: stabilize testing pipeline and clean up technical debt

[code-with-idrees]

Description

This pull request brings significant improvements to the DeepTutor core test suite and resolves underlying technical debt across various modules. By addressing legacy pathing issues, lazy-loading configuration loggers, adding robust retry mechanisms to LLM JSON parsing, and implementing parser support for <think> tags, it completely stabilizes the testing CI/CD pipeline and prevents import-time collection crashes.

Related Issues

• Resolves test suite runner crashes and JSON parsing failures in the reporting agents.

Module(s) Affected

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

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

This PR specifically implements lazy configuration loading in knowledge.py and solve.py to prevent Pytest from throwing FileNotFoundError during collection. It also retroactively applies correct __init__.py files to test subdirectories for valid discovery, updates deprecated RAG flags in test assertions, and adds a robust triple-retry feedback loop in the Reporting Agent to automatically enforce LLM JSON schema validations.