Description of problem:

 
There is a weird behaviour in apps that have both maven and gradle:
 
I took the spring-petclinic as an example and I manually downloaded the code to a folder and cloned it to a different one.
 
The one that I cloned works as expected, but the one that I manually downloaded doesn't match any custom rule. In this last case I can see that the .classpath file is not generated.When looking at the .project file, the cloned app displays both "natures"
 
 

<natures>     
<nature>org.eclipse.jdt.core.javanature</nature>                                      <nature>org.eclipse.buildship.core.gradleprojectnature</nature> 
</natures>

 
But the downloaded app displays gradle only
 
 

<natures> 
<nature>org.eclipse.buildship.core.gradleprojectnature</nature>
</natures>  

 
If I manually remove all the gradle files from the project leaving just maven files, everything works as expected and the rules match.
 

I'm attaching both apps (cloned and downloaded), their respective reports and the custom rule I used to test this