I am new to Symfony and started doing some tutorials in order to get some things done. I am working on a Linux Mint 18 machine and a standard Symfony3-project.
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My knowledge of MySQL suggests one variant which might happen and explain this:
You had (old) mysqld running, then deleted out all files from datadir. Then probably new server wasn't able to start up Then you connected to that old mysqld, which is still running, but getting 'No such file or directory' error trying to access own system files (which were deleted).