Php error when app/themes or app/plugins directories are not empty

  1. Considering your site is installed and working, this is irrelevant. Especially because it seems you’re using bedrock-ansible? It takes care of everything for you. The README for Bedrock talks about a manual install process. It should be updated to referenced bedrock-ansible at some point.

  2. Symlink, yes. And yes it’s supposed to happen. You can access that file by running vagrant ssh. It exists solely on the VM.

  3. These are known errors. Once you add a theme or plugin, WordPress then checks for updates for them. The update requests take too long to complete for some reason through Vagrant and they time out causing those errors. Nothing is technically broken beyond it being slower and annoying. See this thread for more details: Suppressing no connection to wordpress.org error message