Finish/fix migration to Mongodb 3

[adrienjoly]

TODO

• [ ] fix circular dependencies (see warnings included below)
• [ ] DeprecationWarning: collection.ensureIndex is deprecated. Use createIndexes instead.
• [ ] in calls to find(): fields: --> projection:
• [ ] remove remaining references to deprecated functions (e.g. count() and remove())

Refs:

• node-mongodb-native/CHANGES_3.0.0.md at 3.6 · mongodb/node-mongodb-native
• https://mongodb.github.io/node-mongodb-native/3.6/api/
• fix: Improve use of MongoDB 3 (wip)
• notes from fix(mongodb): prevent "db.collections is not a function" error by adrienjoly · Pull Request #232 · openwhyd/openwhyd

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[adrienjoly]

After migrating to mongodb client v3 (see PRs #356 and #355, running in production for 2 days), we're getting the following warnings (and probably many others):

❌ Error -- Sun, 08 Nov 2020 13:49:17 GMT (node:4241) Warning: Accessing non-existent property 'count' of module exports inside circular dependency
(Use `node --trace-warnings ...` to show where the warning was created)
❌ Error -- Sun, 08 Nov 2020 13:49:17 GMT (node:4241) Warning: Accessing non-existent property 'findOne' of module exports inside circular dependency
❌ Error -- Sun, 08 Nov 2020 13:49:17 GMT (node:4241) Warning: Accessing non-existent property 'remove' of module exports inside circular dependency
❌ Error -- Sun, 08 Nov 2020 13:49:17 GMT (node:4241) Warning: Accessing non-existent property 'updateOne' of module exports inside circular dependency

...as spotted in https://github.com/openwhyd/openwhyd/runs/1370367735#step:10:40.

[adrienjoly]

Done in #630.