docs: fix MCP configuration paths and document platform differences

[Chebaleomkar]

Description

This PR fixes configuration issues and path documentation for MCP servers, specifically addressing mismatches when running on Windows. It standardized configuration to use uv run for better cross-platform compatibility and updates documentation to guide users through environment-specific path requirements.

Type of Change

• Bug fix (non-breaking change that fixes an issue)
• New feature (non-breaking change that adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• Documentation update
• Refactoring (no functional changes)

Related Issues

Fixes #3484

Changes Made

• Standardized MCP Config: Updated .mcp.json and .cursor/mcp.json to use uv run. This eliminates the need for platform-specific binary paths (e.g., bin/python vs Scripts/python.exe).
• Improved Documentation: Added a specific section in ENVIRONMENT_SETUP.md explaining how to configure MCP servers manually on both Windows and Linux/macOS.
• Enhanced PYTHONPATH: Added explicit PYTHONPATH exports in the MCP server configurations to ensure cross-package discovery (linking core and tools) works out of the box.

Testing

• Unit tests pass (N/A for docs, but verified uv run logic locally)
• Lint passes (N/A for config/docs)
• Manual testing performed: Verified that the uv run command successfully spawns the MCP server on Windows, whereas the old .venv/bin/python path failed.

Checklist

• My code follows the project's style guidelines
• I have performed a self-review of my code
• I have made corresponding changes to the documentation
• My changes generate no new warnings
• New and existing unit tests pass locally with my changes

Screenshots (if applicable)

(None required for documentation and configuration fixes)

[Som-0619]

can i work on this to complete the remaining tasks....need assign tag

[Cn8001]

This PR does not completely solves the issue. I think it occurs mainly because of claude code's bug as well as Python path. I can continue and change the configuration according to related issues #3484 and #2903,needed assignment. @bryanadenhq

[Chebaleomkar]

I have reproduced the bug and wrote tests . @bryanadenhq @Cn8001

[Cn8001]

@Chebaleomkar , sure it was same for me, but sometimes claude code ignores/crashes when "cwd" option is there and that breaks it again as seen in this bug.

[PatrickChen928]

Thanks for your contribution.
This issue should have been fixed in #3455