Very first commit to default branch didn't close referenced issue

Summary

Based on docs http://docs.gitlab.com/ce/customization/issue_closing.html
when I commit with fix #x in commit message the issue automatically closes if done via gilab UI
but doesn't close when manually committed and pushed with message

Let me know if you guys can reproduce the bug Thx

cc @ayufan @markpundsack

Steps to Reproduce

• Create a new project
• Create a new issue
• Push a commit referencing the above issue's id to the default branch
• E.g. Closes #1

Expected result

• Referenced issue is closed

Actual Result

• Referenced issue remains open and no note is added to the issue

Additional Detail

• GitLab.com project used to reproduce: https://gitlab.com/issue-reproduce/close-issue-first-commit

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Axil: This is by design, solution in this comment: https://gitlab.com/gitlab-org/gitlab-ce/issues/20930#note_14443364