EE’s Matt helped track it down:
Turned out a reference to cache was in the gitignore that stopped the cache library from being committed, then when cloning the repo he no longer had it (in case anyone else hits this issue at some point).
I’ve seen other cases where server settings automatically remove certain file types via security settings- .phar files in particular. If really weird things are happening, make sure the file exists and if it doesn’t, seeing if something is removing it/preventing it from being uploaded is a good idea. It’s rare, but it happens.
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