Restructure credentials after environment overrides.

Follow up to: e0d3313

- Revert renames from `encrypted` and `encrypted_file` back to `credentials`.
  They might be using our Encrypted* generators but from that level of abstraction
  they're still about credentials.

- Same vein: extract a `credentials` method for the `encrypted` local variable. But
  don't call it `encrypted` just because it uses that under the hood. It's about
  capturing the credentials. It's also useful in `change_credentials_in_system_editor`.

- Remove lots of needless argument passing. We've abstracted content_path and key_path
  into methods for a reason, so they should be used. Also spares a conspicuous rename
  of content_path into file_path in other methods.

- Reorders private methods so they're grouped into: command building blocks, option
  parsers, and the generators.

- Extracts commonality in the credentials application tests. A tad unsure about this.
  But I do like that we go with key, content thus matching the command and remove the
  yield which isn't really needed.

- Moves test/credentials_test.rb to beneath the test/application directory. It's a
  Rails application test, so it should be in there.

- Uses `root.join` — a neat trick gleaned from the tests! — and composes the configuration
  private methods such that the building block is below the callers.

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