Add a struct indicating if some Runtime fields were set

To configure runtime fields from the database, we need to know
whether they were explicitly overwritten by the user (we don't
want to overwrite anything that was explicitly set). Store a
struct containing whether the variables we'll grab from the DB
were explicitly set by the user so we know what we can and can't
overwrite.

This determines whether libpod runtime and static dirs were set
via config file in a horribly hackish way (double TOML decode),
but I can't think of a better way, and it shouldn't be that
expensive as the libpod config is tiny.

Signed-off-by: Matthew Heon <mheon@redhat.com>

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