tt clean should remove empty config dirs left after vshard bootstrap

[psergee]

If there are empty directories left after tt clean (create by vshard bootstraping):

├── var
│   ├── lib
│   │   └── tarantool_column_store
│   │       ├── r-1
│   │       │   ├── config
│   │       │   └── config.backup
│   │       └── s1-1
│   │           ├── config
│   │           └── config.backup

Subsequent start and --bootstrap-vshard fails with the following error:
Failed to get current topology replicasets: Failed to get current topology: [string "local function func(...) local cartridge = re..."]:1: section vshard must be a table

Removing empty 'config' directories fixes this issue.