XF 2.0 Upgrade error XF1 to XF2- "do not appear to have the expected contents"

So I followed the instructions for the upgrade from XF1 to XF2. This is what pops up.

There are at least 1 file(s) that do not appear to have the expected contents.Reupload the XenForo files and refresh this page.Only continue if you are sure all files have been uploaded properly.

Screen Shot 2017-12-05 at 8.24.54 AM.webp
 
I'm having the same issue but it's "3 file(s) that do not appear to have the expected contents." I've downloaded the most recent zip archive from my customer area (15 mins ago).

Please advise.
 
When I did a file health check, I see that the following are missing:

Code:
src/vendor/braintree/braintree_php/.github/ISSUE_TEMPLATE.md Missing

src/vendor/braintree/braintree_php/.github/PULL_REQUEST_TEMPLATE.md
 
If it's just those 2 files, technically you can disregard it. I guess your FTP client is potentially ignoring hidden/dot files and directories.
 
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