Reduce npm install time by bundling non-native dependencies

## Problem

The `harperdb` npm package is bundled and minified, but installation is still noticeably slow because npm still resolves and downloads all listed dependencies at install time.

## Proposed

Bundle non-native (pure-JS) dependencies directly into the package bundle and remove them from `dependencies`, so they no longer need to be resolved at install time. Native dependencies (platform-specific binaries) remain as-is. Apply tree-shaking to reduce bundle size further.

Result: only native addons trigger npm resolution; everything else ships pre-bundled.

🤖 Filed by Claude on behalf of Kris.