Generate gem specific sources in lockfile

[soutaro]

The gem specific sources are ignored when:

• The gem X is a dependency of another gem Y that is also listed in gems section prior to the gem

For example:

gems:
  - name: X
  - name: Y
    source:
      type: git
      ...

1. X is added to the lockfile before Y
2. The source definition of Y is ignored because it's traversed as a dependency of X
3. Y is skipped from the gems section, because it's already added to the lockfile (without custom source section)

This PR fixes the problem by introducing gem_entries hash and referees the ignore and source attribute through it instead of passing it as method arguments.