allow user to set prune yes/no

[zlafil]

Allows the user to set a boolean if pruning should be done or not, default true

[jonaskello]

Looks good. I think we can do one more thing to simplify the code. This part:

// Handle the save parameter, delete or rename the temp-files
// This handling only apply to root.json
if (saveQueryParam === "ifcomplete" || saveQueryParam === "no") {
  if (saveQueryParam === "ifcomplete" && missingFilesResult.missingFiles.length === 0) {
    // some code
  } else {
    // Delete files
  }
}

Would probably be simpler to understand if we do this instead (which I think would be the same?):

// The uploaded files have temp file names so they are not "saved" yet.
// Handle the save parameter, delete or rename the temp-files
if (saveQueryParam === "ifcomplete" && missingFilesResult.missingFiles.length === 0) {
  // This handling only apply to root.json
  // Commit temp files ("save" them)
} else if (saveQueryParam === "no") {
  // Delete the temp-files (do not "save" them)
}

[jonaskello]

Perhaps we should make a separate PR for the above changes to not mix them with these.

[jonaskello]

@zlafil Could you also update the changelog in this PR? Add a short description of under the unreleased heading and reference this PR.