Rebuild caches before running updates. #652
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Apparently, Drupal core caches service definitions (in *.services.yml). If a module updates its definitions, the caches need to be manually rebuilt. Fortunately, we already rebuild caches as the last update step, but if the offending module is called as part of the update process itself (i.e. Features), the whole update fails.
See https://www.drupal.org/node/2826466
Simply rebuilding caches as the first step should fix this.