Add option to set runtime flags (#2239)

For istio/istio#37202 I was originally going to use env var hacks - we already have similar for `ISTIO_META` and `XDS_HEADER`. However, envoy runtime vars take the format of `foo.bar_baz=something`. Env vars do not allow `.`, or really any special charecters other than `_`, so we cannot easily use them. Instead, seems better to have an explicit field.
istio · Feb 9, 2022 · 6c56022 · 6c56022
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diff --git a/mesh/v1alpha1/istio.mesh.v1alpha1.gen.json b/mesh/v1alpha1/istio.mesh.v1alpha1.gen.json
diff --git a/mesh/v1alpha1/istio.mesh.v1alpha1.pb.html b/mesh/v1alpha1/istio.mesh.v1alpha1.pb.html