The tool can be explicitly specified in the Application custom resource like this:
```
apiVersion: argoproj.io/v1alpha1
kind: Application
metadata:
...
spec:
...
source:
...
# Tool -> plain directory
directory:
recurse: true
...
```
You also can select the tool in the Application creation wizard in the web user interface. The default is 'Directory'. Press the dropdown button beneath the tool name if you want to choose a different one.