Clean up useless files after Gemfile refactor

Related issue: #3165 (closed)

What does this MR do and why?

Clean up useless files after Gemfile refactor.

• Remove useless files;
• Fix error doc;
• Update related doc to new flow;

New flow example:

• Code sync job: https://jihulab.com/gitlab-cn/code-sync/-/jobs/8815104
• Gemfile.lock updated commit: https://jihulab.com/gitlab-cn/gitlab/-/commits/4037c5ef4e93fd8266a0d72f52a62f9715d7ff23

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