[codex] Manage npm and bun tools locally

[halkn]

Summary

• Install npm and Bun tools into ptm-managed tool directories instead of global package directories.
• Link package binaries from node_modules/.bin into $XDG_BIN_HOME and record npm/Bun package metadata.
• Keep pinned npm/Bun versions consistent across install, check, and update behavior.
• Document the managed npm/Bun layout and clean behavior.

Validation

• uv run pytest
• uv run ruff check src tests
• uv run ruff format --check src tests
• uv run ty check src tests
• git diff --check