Write docs to do collection and project collection

- docs are written to project collection then doc collection

- deletes used to insert into doc collection, now its the same upsert
with deleted = true

- does not set delted = false for new docs as it is not needed, save space

- changed delete to be seperate update on mongo

services/docstore/app/coffee/DocManager.coffee

@@ -2,6 +2,7 @@ MongoManager = require "./MongoManager"
 Errors = require "./Errors"
 logger = require "logger-sharelatex"
 _ = require "underscore"
+async = require "async"
 
 module.exports = DocManager =
 	getDoc: (project_id, doc_id, options, callback = (error, doc, mongoPath) ->) ->
@@ -51,7 +52,13 @@ module.exports = DocManager =
 					newDocLines: lines
 					rev: doc.rev
 				}, "updating doc lines"
-				MongoManager.updateDoc project_id, mongoPath, lines, (error) ->
+				async.series [
+					(cb)->
+						# project collection is still primary so that needs to be successful first
+						MongoManager.updateDoc project_id, mongoPath, lines, cb
+					(cb)->
+						MongoManager.upsertIntoDocCollection project_id, doc_id, lines, doc.rev, cb
+				], (error)->
 					return callback(error) if error?
 					callback null, true, doc.rev + 1 # rev will have been incremented in mongo by MongoManager.updateDoc
 
@@ -59,9 +66,10 @@ module.exports = DocManager =
 		DocManager.getDoc project_id, doc_id, (error, doc) ->
 			return callback(error) if error?
 			return callback new Errors.NotFoundError("No such project/doc: #{project_id}/#{doc_id}") if !doc?
-			MongoManager.insertDoc project_id, doc_id, { lines: doc.lines, deleted: true }, (error) ->
-				return callback(error) if error?
-				callback()
+			MongoManager.upsertIntoDocCollection project_id, doc_id, doc.lines, doc.rev, (error) ->
+				MongoManager.markDocAsDeleted doc_id, (error) ->
+					return callback(error) if error?
+					callback()
 
 	findAllDocsInProject: (project, callback = (error, docs) ->) ->
 		callback null, @_findAllDocsInFolder project.rootFolder[0]

services/docstore/app/coffee/MongoManager.coffee

@@ -18,7 +18,18 @@ module.exports = MongoManager =
 
 		db.projects.update _id: ObjectId(project_id), update, callback
 
-	insertDoc: (project_id, doc_id, attributes, callback = (error) ->) ->
-		attributes._id = ObjectId(doc_id)
-		attributes.project_id = ObjectId(project_id)
-		db.docs.insert attributes, callback
+	upsertIntoDocCollection: (project_id, doc_id, lines, oldRev, callback)->
+		update =
+			$set:{}
+		update.$set["lines"] = lines
+		update.$set["project_id"] = ObjectId(project_id)
+		update.$set["rev"] = oldRev + 1
+		db.docs.update _id: ObjectId(doc_id), update, {upsert: true}, callback
+
+
+	markDocAsDeleted: (doc_id, callback)->
+		update =
+			$set: {}
+		update.$set["deleted"] = true
+		db.docs.update _id: ObjectId(doc_id), update, (err)->
+			callback(err)