docs: use bundle config set instead of install --with

[tnir]

Goal

Force developers not to use bundle install --with and bundle install --binstubs, which were already deprecated.

Design

• Replace bundle install --with with bundle config set with.
• bundle binstubs --all, which is the replacement of bundle install --binstubs, is not mandatory at all in this case.

Changeset

• Replace bundle install --with with bundle config set with.
• Remove bundle install --binstubs.

Testing

• Tested this on my local