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dir: Use system helper to create system repo if necessary
Previously, if /var/lib/flatpak didn't exist then we would use the
system helper to create and populate it, but if it existed and was empty,
we could only populate it if we had privileges. This led to errors from
libostree:
Creating repo: mkdirat: Permission denied
The EnsureRepo method call is allowed by default for active local users,
so do this even if allow_empty is true: this will incorporate
/etc/flatpak/remotes.d into the repository, whether it is newly-created
or not. This makes a `flatpak search` work immediately, without having
to fetch metadata explicitly.
Signed-off-by: Simon McVittie <smcv@collabora.com>
(cherry picked from commit 2489b915ef)
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