[2.1] Fixes for FilePRG bugs when using nested form elements

Encountered issues when using the FilePRG plugin with nested fieldsets/elements. Previously uploaded files were being duplicated in the data, or being removed completely.

Can be verified/tested against the new "FilePRG Plugin Example with nested Fieldset" in https://github.com/cgmartin/ZF2FileUploadExamples.

Also some misc cleanup with comments, and replaced `Form` typehinting with `FormInterface`.