make upload also work with manifest not generated via php

[pablomaurer]

comparing logic:

• hashLocal != hashRemote -> file changed (but local or remote?) -> handle as remote
• if entry in local manifest BUT not in remote manifest -> delete / new local file -> handle as delete
• if entry in remote but not in local -> new remote file
• if local file found not in local manifest -> new local file

But on the second time running this function, and you did not update the manifest, the files are getting uploaded again. I can also not add them to the local file manifest, because it would then delete the new local files.

Maybe it would general be easier to compare lastModified instead hashes, if it's even possible to get everywhere these values?

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Since I currently prefer to use the php manifest version, this Issue does not affect me. But feel free to find a solution yourself and send a PR.