diff --git a/services/web/app/coffee/Features/References/ReferencesHandler.coffee b/services/web/app/coffee/Features/References/ReferencesHandler.coffee
index c033a4999f..7894ab6915 100644
--- a/services/web/app/coffee/Features/References/ReferencesHandler.coffee
+++ b/services/web/app/coffee/Features/References/ReferencesHandler.coffee
@@ -16,19 +16,31 @@ module.exports = ReferencesHandler =
 	_buildDocUrl: (projectId, docId) ->
 		"#{settings.apis.docstore.url}/project/#{projectId}/doc/#{docId}/raw"
 
+	_buildFileUrl: (projectId, fileId) ->
+		"#{settings.apis.filestore.url}/project/#{projectId}/file/#{fileId}"
+
+	_findBibFileIds: (project) ->
+		ids = []
+		_process = (folder) ->
+			(folder.fileRefs or []).forEach (file) ->
+				if file?.name?.match(/^.*\.bib$/)
+					ids.push(file._id)
+			(folder.folders or []).forEach (folder) ->
+				_process(folder)
+		(project.rootFolder or []).forEach (rootFolder) ->
+			_process(rootFolder)
+		return ids
+
 	_findBibDocIds: (project) ->
 		ids = []
-
 		_process = (folder) ->
 			(folder.docs or []).forEach (doc) ->
 				if doc?.name?.match(/^.*\.bib$/)
 					ids.push(doc._id)
 			(folder.folders or []).forEach (folder) ->
 				_process(folder)
-
 		(project.rootFolder or []).forEach (rootFolder) ->
 			_process(rootFolder)
-
 		return ids
 
 	_isFullIndex: (project, callback = (err, result) ->) ->
@@ -43,16 +55,17 @@ module.exports = ReferencesHandler =
 				return callback(err)
 			logger.log {projectId}, "indexing all bib files in project"
 			docIds = ReferencesHandler._findBibDocIds(project)
-			ReferencesHandler._doIndexOperation(projectId, project, docIds, callback)
+			fileIds = ReferencesHandler._findBibFileIds(project)
+			ReferencesHandler._doIndexOperation(projectId, project, docIds, fileIds, callback)
 
 	index: (projectId, docIds, callback=(err, data)->) ->
 		ProjectGetter.getProject projectId, {rootFolder: true, owner_ref: 1}, (err, project) ->
 			if err
 				logger.err {err, projectId}, "error finding project"
 				return callback(err)
-			ReferencesHandler._doIndexOperation(projectId, project, docIds, callback)
+			ReferencesHandler._doIndexOperation(projectId, project, docIds, [], callback)
 
-	_doIndexOperation: (projectId, project, docIds, callback) ->
+	_doIndexOperation: (projectId, project, docIds, fileIds, callback) ->
 		ReferencesHandler._isFullIndex project, (err, isFullIndex) ->
 			if err
 				logger.err {err, projectId}, "error checking whether to do full index"
@@ -67,11 +80,14 @@ module.exports = ReferencesHandler =
 						return callback(err)
 					bibDocUrls = docIds.map (docId) ->
 						ReferencesHandler._buildDocUrl projectId, docId
+					bibFileUrls = fileIds.map (fileId) ->
+						ReferencesHandler._buildFileUrl projectId, fileId
+					allUrls = bibDocUrls.concat(bibFileUrls)
 					logger.log {projectId, isFullIndex, docIds, bibDocUrls}, "sending request to references service"
 					request.post {
 						url: "#{settings.apis.references.url}/project/#{projectId}/index"
 						json:
-							docUrls: bibDocUrls
+							docUrls: allUrls
 							fullIndex: isFullIndex
 					}, (err, res, data) ->
 						if err
diff --git a/services/web/public/coffee/ide/references/ReferencesManager.coffee b/services/web/public/coffee/ide/references/ReferencesManager.coffee
index b0f49f54f8..2f1e95c5b1 100644
--- a/services/web/public/coffee/ide/references/ReferencesManager.coffee
+++ b/services/web/public/coffee/ide/references/ReferencesManager.coffee
@@ -11,6 +11,9 @@ define [
 					if entity?.name?.match /.*\.bib$/
 						@indexReferences([doc.doc_id], true)
 
+			@$scope.$on 'references:should-reindex', (e, data) =>
+				@indexAllReferences(true)
+
 			# When we join the project:
 			#   index all references files
 			#   and don't broadcast to all clients
diff --git a/services/web/test/UnitTests/coffee/References/ReferencesHandlerTests.coffee b/services/web/test/UnitTests/coffee/References/ReferencesHandlerTests.coffee
index 53e064d821..c46e71a542 100644
--- a/services/web/test/UnitTests/coffee/References/ReferencesHandlerTests.coffee
+++ b/services/web/test/UnitTests/coffee/References/ReferencesHandlerTests.coffee
@@ -21,7 +21,11 @@ describe 'ReferencesHandler', ->
 					{name: 'two.txt', _id: 'bbb'},
 				]
 				folders: [
-					{docs: [{name: 'three.bib', _id: 'ccc'}], folders: []}
+					{
+						docs: [{name: 'three.bib', _id: 'ccc'}],
+						fileRefs: [{name: 'four.bib', _id: 'ghg'}],
+						folders: []
+					}
 				]
 			]
 		@docIds = ['aaa', 'ccc']
@@ -34,6 +38,7 @@ describe 'ReferencesHandler', ->
 				apis:
 					references: {url: 'http://some.url/references'}
 					docstore: {url: 'http://some.url/docstore'}
+					filestore: {url: 'http://some.url/filestore'}
 			}
 			'request': @request = {
 				get: sinon.stub()
@@ -56,6 +61,7 @@ describe 'ReferencesHandler', ->
 
 		beforeEach ->
 			sinon.stub(@handler, '_findBibDocIds')
+			sinon.stub(@handler, '_findBibFileIds')
 			sinon.stub(@handler, '_isFullIndex').callsArgWith(1, null, true)
 			@request.post.callsArgWith(1, null, {statusCode: 200}, @fakeResponseData)
 			@call = (callback) =>
@@ -198,6 +204,7 @@ describe 'ReferencesHandler', ->
 
 		beforeEach ->
 			sinon.stub(@handler, '_findBibDocIds').returns(['aaa', 'ccc'])
+			sinon.stub(@handler, '_findBibFileIds').returns(['fff', 'ggg'])
 			sinon.stub(@handler, '_isFullIndex').callsArgWith(1, null, true)
 			@request.post.callsArgWith(1, null, {statusCode: 200}, @fakeResponseData)
 			@call = (callback) =>
@@ -209,6 +216,12 @@ describe 'ReferencesHandler', ->
 				@handler._findBibDocIds.calledWith(@fakeProject).should.equal true
 				done()
 
+		it 'should call _findBibFileIds', (done) ->
+			@call (err, data) =>
+				@handler._findBibDocIds.callCount.should.equal 1
+				@handler._findBibDocIds.calledWith(@fakeProject).should.equal true
+				done()
+
 		it 'should call DocumentUpdaterHandler.flushDocToMongo', (done) ->
 			@call (err, data) =>
 				@DocumentUpdaterHandler.flushDocToMongo.callCount.should.equal 2
@@ -219,7 +232,7 @@ describe 'ReferencesHandler', ->
 				@request.post.callCount.should.equal 1
 				arg = @request.post.firstCall.args[0]
 				expect(arg.json).to.have.all.keys 'docUrls', 'fullIndex'
-				expect(arg.json.docUrls.length).to.equal 2
+				expect(arg.json.docUrls.length).to.equal 4
 				expect(arg.json.fullIndex).to.equal true
 				done()
 
@@ -309,6 +322,32 @@ describe 'ReferencesHandler', ->
 			result = @handler._findBibDocIds(@fakeProject)
 			expect(result).to.deep.equal @expectedIds
 
+	describe '_findBibFileIds', ->
+
+		beforeEach ->
+			@fakeProject =
+				rootFolder: [
+					docs: [
+						{name: 'one.bib', _id: 'aaa'},
+						{name: 'two.txt', _id: 'bbb'},
+					]
+					fileRefs: [
+						{name: 'other.bib', _id: 'ddd'}
+					],
+					folders: [
+						{
+							docs: [{name: 'three.bib', _id: 'ccc'}],
+							fileRefs: [{name: 'four.bib', _id: 'ghg'}],
+							folders: []
+						}
+					]
+				]
+			@expectedIds = ['ddd', 'ghg']
+
+		it 'should select the correct docIds', ->
+			result = @handler._findBibFileIds(@fakeProject)
+			expect(result).to.deep.equal @expectedIds
+
 	describe '_isFullIndex', ->
 
 		beforeEach ->