fix(cli): include source for file-pinned nodes

[Inference1]

Summary

• enable source output when codegraph node <symbol> -f <file> disambiguates a symbol
• preserve existing file-only and bare-symbol behavior
• add end-to-end regression coverage with two same-named definitions

Root cause

The CLI passed symbol and file for a file-pinned lookup but omitted includeCode: true, so the MCP handler correctly selected the definition while rendering it without its body.

Testing

• npm run build
• full Vitest suite: 139 files passed, 2,375 tests passed, 4 skipped

Fixes #1284