Fix queries on collection's elements with MongoDB

How to reproduce:

• set up a Nuxeo instance with hot fixes up to 39 (not sure if this is important) and mongodb as backend database
• create a File document in a workspace
• add the File document to a new *collection collection1
• XML export of Collection1 shows the document reference of the File document in field collection:documentIds
• permanently delete the File document

document reference of the File document is not removed from field collection:documentIds. This only happens with mongodb, the document reference is properly removed with PostGreSQL.

I also noticed that the content view used for a collection does not list any document even when having member documents, could be a side effect of the bug.
Automation operation Collection.GetDocumentsFromCollection executed on the collection return an empty list of documents.

Find below docker-compose files to set up the necessary test Nuxeo instance:

NUXEO_CLID=<VALID_CLID_HERE>

version: '2'
    
services:
  mongodb:
    image: mongo:2.6.5
    command: --smallfiles
    ports:
      - "27017:27017"

  nuxeo:
    image: nuxeo:6.0
    env_file: .env
    environment:
      - NUXEO_DEV_MODE=true
      - NUXEO_INSTALL_HOTFIX=false
      - NUXEO_PACKAGES=nuxeo-6.0-HF39 nuxeo-dam nuxeo-diff nuxeo-csv platform-explorer nuxeo-platform-importer
      - NUXEO_TEMPLATES=default,mongodb
      - NUXEO_CUSTOM_PARAM=nuxeo.mongodb.server=mongodb:27017
    ports:
      - "8080:8080"