Fix non-bazel & bazel file query error #9
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When we mix files that are tracked by Bazel with files that are not tracked by Bazel,
bazel queryfails. Even with--keep-goingenabled we are getting a non zero exit code and that is preventing us from reading from our output proto stream.This stopgap solution should be fine for now. We need to find a way to get back to our optimized query
Fixes #8