runtime: Correctly handle data dirs when in a Flatpak environment
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Expose the modified /app to the subsandbox, if any
If we modify "/app" we want to bind it to the new subsandbox instead of always binding an empty directory.
When we are in a Flatpak environment there are two issues:
For this reason we avoid raising a warning if we have multiple data directory and also we bind them preserving their original path.