Add configurable language extension mapping

[lzehrung]

Summary

• Adds languages.extensions to codegraph.config.json for suffix-to-language mappings.
• Threads mappings through discovery, indexing, graph extraction, import collection, bloom/module cache signatures, sessions, and CLI build options.
• Documents extension mapping in README, CLI docs, and the Codegraph skill.

Verification

• rtk npx vitest run tests/codegraph-config.test.ts
• rtk npm run build
• rtk npm run check