Repro steps:

1. run gradle eclipse for the first time against a project
2. notice resulting .project file

   <projectDescription>
     <name>
       helloworld
     </name>
     <comment/>
     <projects/>
     <natures>
       <nature>
         org.eclipse.jdt.core.javanature
       </nature>
     </natures>
     <buildSpec>
       <buildCommand>
         <name>
           org.eclipse.jdt.core.javabuilder
         </name>
         <arguments/>
       </buildCommand>
     </buildSpec>
     <links/>
   </projectDescription>
   

3. within eclipse, add a project nature (in this case, STS's 'Spring Project Nature'
4. notice the resulting file and it's formatting differences

   <?xml version="1.0" encoding="UTF-8"?>
   <projectDescription>
           <name>helloworld</name>
           <comment></comment>
           <projects>
           </projects>
           <buildSpec>
                   <buildCommand>
                           <name>org.eclipse.jdt.core.javabuilder</name>
                           <arguments>
                           </arguments>
                   </buildCommand>
                   <buildCommand>
                           <name>org.springframework.ide.eclipse.core.springbuilder</name>
                           <arguments>
                           </arguments>
                   </buildCommand>
           </buildSpec>
           <natures>
                   <nature>org.springframework.ide.eclipse.core.springnature</nature>
                   <nature>org.eclipse.jdt.core.javanature</nature>
           </natures>
   </projectDescription>
   

5. assume the user checks in at this point
6. assume the user later runs gradle eclipse again
7. notice that the spring nature is preserved, but formatting is not