Fix issue with github storage running in non-empty directories

[cicdw]

When running a deployment within a Docker image that has a non-empty working directory, GitHub storage would fail because git clone errors out if the directory is non-empty. This PR adjusts the logic to git clone into a temporary directory (that will always be empty) and then recursively copy all files over into the present working directory. This code path is the same as if a user had specified a subdirectory of their repository, so a nice side effect is a unified code path.

QA'ed live with @discdiver @WillRaphaelson and @khuyentran1401

Checklist

• This pull request references any related issue by including "closes <link to issue>"
  • If no issue exists and your change is not a small fix, please create an issue first.
• This pull request includes tests or only affects documentation.
• This pull request includes a fix, feature, enhancement, docs, or maintenance label categorizing the change.

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