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Hold option and click on the “collapse file” button in the Files view of a commit or pull request, and it will collapse all the files.
Select text in a comment, issue, or pull request description and press r—the selected text (including markdown formatting) will get pre-populated as a markdown block quote reply in the next comment box.
Add .patch or .diff to any pull request URL if you want to see a plain-text diff of the pull request (e.g. maybe you want to quickly `curl ... | git apply -` an unmerged pull request into a local copy of the repo without trying to add and fetch the git remote that the pull request is from).
There are lots of keyboard shortcuts. For example, / to jump to the file finder.
Not so much a secret but more like a hiding in plain sight: when looking at a commit GitHub will show you the earliest and latest tag (i.e. release) that includes the commit. For example, this commit[1] first appeared in v3_2_0_preview3.
[1]: https://github.com/ruby/ruby/commit/892f350a7db4d2cc99c5061d...