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flatpak: Use new flatpak API to automatically remove EOL runtimes

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Merged Kalev Lember requested to merge wip/kalev/flatpak-eol-runtime-cleanup into master Oct 15, 2020
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When constructing the update transaction, tell flatpak that it can clean up unused EOL runtimes during the transaction.

We don't have any UI for that, which hopefully should be fine.

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Source branch: wip/kalev/flatpak-eol-runtime-cleanup