pruneGeneratedFiles is incorrectly deleting files

[calvincestari]

Created from #2546 and comment #2546 (comment).

[AnthonyMDev]

@SilverTab @pchmelar We have still been unable to reproduce the deletion of the files, as we spoke about in #2546. I'm wondering if other fixes we've made since than have inadvertently resolved this issue as well.

Could one of you try turning pruneGeneratedFiles back to true and see if it still deletes the wrong files with the latest version of the CLI?

[pchmelar]

Looks good in 1.0.6 🎉 Thank you!
MateeDevs/devstack-native-app#55

[calvincestari]

Thanks for following up @pchmelar, I'm going to close out this issue now.

If it recurs please do come back to this issue and we'll take up the search again - thanks.

[calvincestari]

Here's some additional debugging from a customer recently:

I think I had found the potential root cause of the issue.
in configs file we were setting the following

"output" : {
    .
    .
    .
    "operations" : {
      "relative" : {
        "subpath" : "./GraphQLOperations"
      }
    }
  },

I think defining the subpath of relative mode for operations files starting with ./ was causing this issue (it was working fine t generate operations models at expected subpath, but on regeneration I think some unexpected behaviour happens and fails to match operation files to query files).
changing to "subpath" : "GraphQLOperations" fixing the issue without the need to disable pruneGeneratedFiles