Refactor package/dependency code to use consistent terminology

Created by: olafurpg

Towards #37990 (closed).

This PR is a pure refactoring. There are no functional differences.

• a "package" refers to an npm/maven/go package/artifact/module
• a "dependency" refers to the dependency relationship between two packages
• distinguish whether a package has a version or not. Previously, we silently used the empty string for versions when it was missing. The distinction is important because we only need a package without versions to create a Sourcegraph repo. The version is needed only when cloning/fetching that repository.

Test plan

See the tests pass.