Remove Repository#root_ref_sha method

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Problem

Bug in NoMethodError: undefined method `sha' for nil:N... (#395480 - closed) exposes the problem with Repository#root_ref_sha method

It doesn't verify that the head commit exist and it leads to NoMethodError.

This method is used across the application.

Proposal

Remove the method completely and replace usages with the code that correctly handles this case.

head_commit = repository.head_commit

if head_commit
  sha = head_commit.sha
  ...

Or alternatively, use head_commit&.sha version. However, we should still verify that it doesn't break existing code.