fix: mongodb repository.find filters soft deleted rows

[spotykatch]

Closes: #7113

Description of change

MongoRepository find, findAndCount, findByIds, findOne methods do not select rows that was soft deleted.

Pull-Request Checklist

• Code is up-to-date with the master branch
• npm run lint passes with this change
• npm run test passes with this change
• This pull request links relevant issues as Fixes #0000
• There are new or updated unit tests validating the change
• Documentation has been updated to reflect this change
• The new commits follow conventions explained in CONTRIBUTING.md

[spotykatch]

Tests are failing with #8567 😄

[pleerock]

Does filter mutate the original cursor ?

[spotykatch]

It does.

Cursor.prototype.filter = function(filter) {
  if(this.s.state == Cursor.CLOSED || this.s.state == Cursor.OPEN || this.isDead()) throw MongoError.create({message: "Cursor is closed", driver:true});
  this.s.cmd.query = filter;
  return this;
}