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flatpak: Fix the build on Aarch64

Mathieu Bridon requested to merge bochecha/flatpak into master

The mtools release is old and predates the Aarch64 support in the autotools.

As a result, the included config.{guess,sub} files do not know about the Aarch64 architecture, and the build fails.

This commit takes some newer config.{guess,sub} files which the Sdk helpfully provides for exactly this purpose.

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