MongoCollection.count() and update() are deprecated

Eve doesn't have any counting methods on `current_app.data`, so there is
no one-to-one translation for `cursor.count()` in
`file_storage/__init__.py`. Since the call was only used in a debug log
entry, I just removed it altogether.

I removed `pillar.cli.operations.index_users_rebuild()`, as it was
importing `pillar.api.utils.algolia.algolia_index_user_save` which doesn't
exist any more, so the code was dead anyway.

tests/test_api/test_comments.py

@@ -81,7 +81,7 @@ class CommentEditTest(AbstractPillarTest):
 
         with self.app.app_context():
             proj_coll = self.app.db('projects')
-            proj_coll.update(
+            proj_coll.update_one(
                 {'_id': self.pid},
                 {'$set': {
                     'node_types': self.project['node_types'],