run: Allow caller to replace /app and/or /usr

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The pressure-vessel container tool in Steam will want to use this, to
replace /usr with a Steam Runtime container supplied by the Steam CDN,
instead of using the same Flatpak runtime that is used to run the Steam
client and non-containerized games.

If a custom /usr is used, the "official" Flatpak runtime is still the
one reflected in the metadata. It is also mounted at /run/parent,
with all its extensions, so that pressure-vessel has the option of using
its graphics drivers (by populating the custom /usr with symlinks into
/run/parent and/or /run/host).

When doing this, we need to put an empty directory on /app, because
the real /app expects to be run on top of the real runtime. It would
also be reasonable to substitute a custom replacement for /app, so
I've included support for that too.

Partially addresses #3797.

Signed-off-by: Simon McVittie <smcv@collabora.com>

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