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_nodes.py

@@ -690,7 +690,7 @@ class NodesReferencedByProjectTest(AbstractPillarTest):
         self.node_etag = node['_etag']
 
         with self.app.app_context():
-            self.app.db('projects').update(
+            self.app.db('projects').update_one(
                 {'_id': self.pid},
                 {'$set': {
                     'header_node': self.node_id,