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Add `tube.upload_manually` to upload files in chunks (#2410)

* Add `tube.upload_manually`

Upload data in chunks when having a tube connected to a shell.
This is useful when doing kernel or qemu challenges where you can't use the ssh tube's file upload features.

* Add tests and fix corner cases

* Update CHANGELOG

* Fix character escaping in tests

* Fix gzip compression on Python 2

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