Remove unused dependencies

Example: `node-gyp` is listed in our package.json and is no longer used. We will use this issue to track completion and identify any unused dependencies to also get rid of.

Related to https://github.com/ChainSafe/lodestar/issues/6026

Dependencies to remove:
- `node-gyp`

Start in package.json and search the repository for node-gyp references to confirm the dependency is unused; review related issue #6026 for context. Done means removing node-gyp and verifying the dependency installation and relevant checks still pass.

Written by the indexing model from the issue text.