diff --git a/app/coffee/CompileController.coffee b/app/coffee/CompileController.coffee
index 250f9b8..f4dcb0e 100644
--- a/app/coffee/CompileController.coffee
+++ b/app/coffee/CompileController.coffee
@@ -4,6 +4,7 @@ Settings = require "settings-sharelatex"
 Metrics = require "./Metrics"
 ProjectPersistenceManager = require "./ProjectPersistenceManager"
 logger = require "logger-sharelatex"
+Errors = require "./Errors"
 
 module.exports = CompileController =
 	compile: (req, res, next = (error) ->) ->
@@ -15,7 +16,10 @@ module.exports = CompileController =
 			ProjectPersistenceManager.markProjectAsJustAccessed request.project_id, (error) ->
 				return next(error) if error?
 				CompileManager.doCompile request, (error, outputFiles = []) ->
-					if error?.terminated
+					if error instanceof Errors.FilesOutOfSyncError
+						code = 409 # Http 409 Conflict
+						status = "retry"
+					else if error?.terminated
 						status = "terminated"
 					else if error?.validate
 						status = "validation-#{error.validate}"
diff --git a/app/coffee/CompileManager.coffee b/app/coffee/CompileManager.coffee
index ae40bf7..56d04db 100644
--- a/app/coffee/CompileManager.coffee
+++ b/app/coffee/CompileManager.coffee
@@ -31,13 +31,17 @@ module.exports = CompileManager =
 
 		timer = new Metrics.Timer("write-to-disk")
 		logger.log project_id: request.project_id, user_id: request.user_id, "syncing resources to disk"
-		ResourceWriter.syncResourcesToDisk request.project_id, request.resources, compileDir, (error) ->
-			if error?
+		ResourceWriter.syncResourcesToDisk request, compileDir, (error, resourceList) ->
+			# NOTE: resourceList is insecure, it should only be used to exclude files from the output list
+			if error? and error instanceof Errors.FilesOutOfSyncError
+				logger.warn project_id: request.project_id, user_id: request.user_id, "files out of sync, please retry"
+				return callback(error)
+			else if error?
 				logger.err err:error, project_id: request.project_id, user_id: request.user_id, "error writing resources to disk"
-				return callback(error) 
+				return callback(error)
 			logger.log project_id: request.project_id, user_id: request.user_id, time_taken: Date.now() - timer.start, "written files to disk"
 			timer.done()
-			
+
 			injectDraftModeIfRequired = (callback) ->
 				if request.draft
 					DraftModeManager.injectDraftMode Path.join(compileDir, request.rootResourcePath), callback
@@ -45,7 +49,7 @@ module.exports = CompileManager =
 					callback()
 
 			createTikzFileIfRequired = (callback) ->
-				if TikzManager.needsOutputFile(request.rootResourcePath, request.resources)
+				if TikzManager.needsOutputFile(request.rootResourcePath, resourceList)
 					TikzManager.injectOutputFile compileDir, request.rootResourcePath, callback
 				else
 					callback()
@@ -91,7 +95,7 @@ module.exports = CompileManager =
 						error.validate = "fail"
 					# compile was killed by user, was a validation, or a compile which failed validation
 					if error?.terminated or error?.validate
-						OutputFileFinder.findOutputFiles request.resources, compileDir, (err, outputFiles) ->
+						OutputFileFinder.findOutputFiles resourceList, compileDir, (err, outputFiles) ->
 							return callback(err) if err?
 							callback(error, outputFiles) # return output files so user can check logs
 						return
@@ -111,7 +115,7 @@ module.exports = CompileManager =
 					if stats?["latex-runs"] > 0 and timings?["cpu-time"] > 0
 						Metrics.timing("run-compile-cpu-time-per-pass", timings["cpu-time"] / stats["latex-runs"])
 
-					OutputFileFinder.findOutputFiles request.resources, compileDir, (error, outputFiles) ->
+					OutputFileFinder.findOutputFiles resourceList, compileDir, (error, outputFiles) ->
 						return callback(error) if error?
 						OutputCacheManager.saveOutputFiles outputFiles, compileDir,  (error, newOutputFiles) ->
 							callback null, newOutputFiles
diff --git a/app/coffee/DraftModeManager.coffee b/app/coffee/DraftModeManager.coffee
index 253cbff..2f9e931 100644
--- a/app/coffee/DraftModeManager.coffee
+++ b/app/coffee/DraftModeManager.coffee
@@ -5,6 +5,9 @@ module.exports = DraftModeManager =
 	injectDraftMode: (filename, callback = (error) ->) ->
 		fs.readFile filename, "utf8", (error, content) ->
 			return callback(error) if error?
+			# avoid adding draft mode more than once
+			if content?.indexOf("\\documentclass\[draft") >= 0
+				return callback()
 			modified_content = DraftModeManager._injectDraftOption content
 			logger.log {
 				content: content.slice(0,1024), # \documentclass is normally v near the top
@@ -18,4 +21,4 @@ module.exports = DraftModeManager =
 			# With existing options (must be first, otherwise both are applied)
 			.replace(/\\documentclass\[/g, "\\documentclass[draft,")
 			# Without existing options
-			.replace(/\\documentclass\{/g, "\\documentclass[draft]{")
\ No newline at end of file
+			.replace(/\\documentclass\{/g, "\\documentclass[draft]{")
diff --git a/app/coffee/Errors.coffee b/app/coffee/Errors.coffee
index 4abea0b..2e3ae75 100644
--- a/app/coffee/Errors.coffee
+++ b/app/coffee/Errors.coffee
@@ -5,6 +5,13 @@ NotFoundError = (message) ->
 	return error
 NotFoundError.prototype.__proto__ = Error.prototype
 
+FilesOutOfSyncError = (message) ->
+	error = new Error(message)
+	error.name = "FilesOutOfSyncError"
+	error.__proto__ = FilesOutOfSyncError.prototype
+	return error
+FilesOutOfSyncError.prototype.__proto__ = Error.prototype
 
 module.exports = Errors =
 	NotFoundError: NotFoundError
+	FilesOutOfSyncError: FilesOutOfSyncError
diff --git a/app/coffee/RequestParser.coffee b/app/coffee/RequestParser.coffee
index 8fc4ecf..596b529 100644
--- a/app/coffee/RequestParser.coffee
+++ b/app/coffee/RequestParser.coffee
@@ -32,6 +32,27 @@ module.exports = RequestParser =
 				compile.options.check,
 				type: "string"
 
+			# The syncType specifies whether the request contains all
+			# resources (full) or only those resources to be updated
+			# in-place (incremental).
+			response.syncType = @_parseAttribute "syncType",
+				compile.options.syncType,
+				validValues: ["full", "incremental"]
+				type: "string"
+
+			# The syncState is an identifier passed in with the request
+			# which has the property that it changes when any resource is
+			# added, deleted, moved or renamed.
+			#
+			# on syncType full the syncState identifier is passed in and
+			# stored
+			#
+			# on syncType incremental the syncState identifier must match
+			# the stored value
+			response.syncState = @_parseAttribute "syncState",
+				compile.options.syncState,
+				type: "string"
+
 			if response.timeout > RequestParser.MAX_TIMEOUT
 				response.timeout = RequestParser.MAX_TIMEOUT
 			response.timeout = response.timeout * 1000 # milliseconds
diff --git a/app/coffee/ResourceListManager.coffee b/app/coffee/ResourceListManager.coffee
new file mode 100644
index 0000000..aef2d2f
--- /dev/null
+++ b/app/coffee/ResourceListManager.coffee
@@ -0,0 +1,25 @@
+Path = require "path"
+fs = require "fs"
+logger = require "logger-sharelatex"
+settings = require("settings-sharelatex")
+SafeReader = require "./SafeReader"
+
+module.exports = ResourceListManager =
+
+	# This file is a list of the input files for the project, one per
+	# line, used to identify output files (i.e. files not on this list)
+	# when the incoming request is incremental.
+	RESOURCE_LIST_FILE: ".project-resource-list"
+
+	saveResourceList: (resources, basePath, callback = (error) ->) ->
+		resourceListFile = Path.join(basePath, @RESOURCE_LIST_FILE)
+		resourceList = (resource.path for resource in resources)
+		fs.writeFile resourceListFile, resourceList.join("\n"), callback
+
+	loadResourceList: (basePath, callback = (error) ->) ->
+		resourceListFile = Path.join(basePath, @RESOURCE_LIST_FILE)
+		# limit file to 128K, compile directory is user accessible
+		SafeReader.readFile resourceListFile, 128*1024, 'utf8', (err, resourceList) ->
+			return callback(err) if err?
+			resources = ({path: path} for path in resourceList?.toString()?.split("\n") or [])
+			callback(null, resources)
diff --git a/app/coffee/ResourceStateManager.coffee b/app/coffee/ResourceStateManager.coffee
new file mode 100644
index 0000000..eb193b8
--- /dev/null
+++ b/app/coffee/ResourceStateManager.coffee
@@ -0,0 +1,45 @@
+Path = require "path"
+fs = require "fs"
+logger = require "logger-sharelatex"
+settings = require("settings-sharelatex")
+Errors = require "./Errors"
+SafeReader = require "./SafeReader"
+
+module.exports = ResourceStateManager =
+
+	# The sync state is an identifier which must match for an
+	# incremental update to be allowed.
+	#
+	# The initial value is passed in and stored on a full
+	# compile.
+	#
+	# Subsequent incremental compiles must come with the same value - if
+	# not they will be rejected with a 409 Conflict response.
+	#
+	# An incremental compile can only update existing files with new
+	# content.  The sync state identifier must change if any docs or
+	# files are moved, added, deleted or renamed.
+
+	SYNC_STATE_FILE: ".project-sync-state"
+
+	saveProjectStateHash: (state, basePath, callback) ->
+		stateFile = Path.join(basePath, @SYNC_STATE_FILE)
+		if not state? # remove the file if no state passed in
+			logger.log state:state, basePath:basePath, "clearing sync state"
+			fs.unlink stateFile, (err) ->
+				if err? and err.code isnt 'ENOENT'
+					return callback(err)
+				else
+					return callback()
+		else
+			logger.log state:state, basePath:basePath, "writing sync state"
+			fs.writeFile stateFile, state, {encoding: 'ascii'}, callback
+
+	checkProjectStateHashMatches: (state, basePath, callback) ->
+		stateFile = Path.join(basePath, @SYNC_STATE_FILE)
+		SafeReader.readFile stateFile, 64, 'ascii', (err, oldState) ->
+			return callback(err) if err?
+			if state isnt oldState
+				return callback new Errors.FilesOutOfSyncError("invalid state for incremental update")
+			else
+				callback(null)
diff --git a/app/coffee/ResourceWriter.coffee b/app/coffee/ResourceWriter.coffee
index e2a0e1f..7f67026 100644
--- a/app/coffee/ResourceWriter.coffee
+++ b/app/coffee/ResourceWriter.coffee
@@ -4,6 +4,8 @@ fs = require "fs"
 async = require "async"
 mkdirp = require "mkdirp"
 OutputFileFinder = require "./OutputFileFinder"
+ResourceStateManager = require "./ResourceStateManager"
+ResourceListManager = require "./ResourceListManager"
 Metrics = require "./Metrics"
 logger = require "logger-sharelatex"
 settings = require("settings-sharelatex")
@@ -11,7 +13,36 @@ settings = require("settings-sharelatex")
 parallelFileDownloads = settings.parallelFileDownloads or 1
 
 module.exports = ResourceWriter =
-	syncResourcesToDisk: (project_id, resources, basePath, callback = (error) ->) ->
+
+	syncResourcesToDisk: (request, basePath, callback = (error, resourceList) ->) ->
+		if request.syncType is "incremental"
+			ResourceStateManager.checkProjectStateHashMatches request.syncState, basePath, (error) ->
+				return callback(error) if error?
+				ResourceListManager.loadResourceList basePath, (error, resourceList) ->
+					return callback(error) if error?
+					ResourceWriter._removeExtraneousFiles resourceList, basePath, (error) =>
+						return callback(error) if error?
+						ResourceWriter.saveIncrementalResourcesToDisk request.project_id, request.resources, basePath, (error) ->
+							return callback(error) if error?
+							callback(null, resourceList)
+		else
+			@saveAllResourcesToDisk request.project_id, request.resources, basePath, (error) ->
+				return callback(error) if error?
+				ResourceStateManager.saveProjectStateHash request.syncState, basePath, (error) ->
+					return callback(error) if error?
+					ResourceListManager.saveResourceList request.resources, basePath, (error) =>
+						return callback(error) if error?
+						callback(null, request.resources)
+
+	saveIncrementalResourcesToDisk: (project_id, resources, basePath, callback = (error) ->) ->
+		@_createDirectory basePath, (error) =>
+			return callback(error) if error?
+			jobs = for resource in resources
+				do (resource) =>
+					(callback) => @_writeResourceToDisk(project_id, resource, basePath, callback)
+			async.parallelLimit jobs, parallelFileDownloads, callback
+
+	saveAllResourcesToDisk: (project_id, resources, basePath, callback = (error) ->) ->
 		@_createDirectory basePath, (error) =>
 			return callback(error) if error?
 			@_removeExtraneousFiles resources, basePath, (error) =>
@@ -48,6 +79,8 @@ module.exports = ResourceWriter =
 					should_delete = true
 					if path.match(/^output\./) or path.match(/\.aux$/) or path.match(/^cache\//) # knitr cache
 						should_delete = false
+					if path in ['.project-resource-list', '.project-sync-state']
+						should_delete = false
 					if path == "output.pdf" or path == "output.dvi" or path == "output.log" or path == "output.xdv"
 						should_delete = true
 					if path == "output.tex" # created by TikzManager if present in output files
diff --git a/app/coffee/SafeReader.coffee b/app/coffee/SafeReader.coffee
new file mode 100644
index 0000000..7ed3693
--- /dev/null
+++ b/app/coffee/SafeReader.coffee
@@ -0,0 +1,24 @@
+fs = require "fs"
+
+module.exports = SafeReader =
+
+	# safely read up to size bytes from a file and return result as a
+	# string
+
+	readFile: (file, size, encoding, callback = (error, result) ->) ->
+		fs.open file, 'r', (err, fd) ->
+			return callback() if err? and  err.code is 'ENOENT'
+			return callback(err) if err?
+
+			# safely return always closing the file
+			callbackWithClose = (err, result) ->
+				fs.close fd, (err1) ->
+					return callback(err) if err?
+					return callback(err1) if err1?
+					callback(null, result)
+
+			buff = new Buffer(size, 0) # fill with zeros
+			fs.read fd, buff, 0, buff.length, 0, (err, bytesRead, buffer) ->
+				return callbackWithClose(err) if err?
+				result = buffer.toString(encoding, 0, bytesRead)
+				callbackWithClose(null, result)
diff --git a/test/unit/coffee/CompileManagerTests.coffee b/test/unit/coffee/CompileManagerTests.coffee
index de33166..ff671b2 100644
--- a/test/unit/coffee/CompileManagerTests.coffee
+++ b/test/unit/coffee/CompileManagerTests.coffee
@@ -51,7 +51,7 @@ describe "CompileManager", ->
 			@env = {}
 			@Settings.compileDir = "compiles"
 			@compileDir = "#{@Settings.path.compilesDir}/#{@project_id}-#{@user_id}"
-			@ResourceWriter.syncResourcesToDisk = sinon.stub().callsArg(3)
+			@ResourceWriter.syncResourcesToDisk = sinon.stub().callsArgWith(2, null, @resources)
 			@LatexRunner.runLatex = sinon.stub().callsArg(2)
 			@OutputFileFinder.findOutputFiles = sinon.stub().callsArgWith(2, null, @output_files)
 			@OutputCacheManager.saveOutputFiles = sinon.stub().callsArgWith(2, null, @build_files)
@@ -64,7 +64,7 @@ describe "CompileManager", ->
 
 			it "should write the resources to disk", ->
 				@ResourceWriter.syncResourcesToDisk
-					.calledWith(@project_id, @resources, @compileDir)
+					.calledWith(@request, @compileDir)
 					.should.equal true
 
 			it "should run LaTeX", ->
diff --git a/test/unit/coffee/RequestParserTests.coffee b/test/unit/coffee/RequestParserTests.coffee
index 1cd931b..0b420b3 100644
--- a/test/unit/coffee/RequestParserTests.coffee
+++ b/test/unit/coffee/RequestParserTests.coffee
@@ -242,3 +242,13 @@ describe "RequestParser", ->
 		it "should return an error", ->
 			@callback.calledWith("relative path in root resource")
 				.should.equal true
+
+	describe "with an unknown syncType", ->
+		beforeEach ->
+			@validRequest.compile.options.syncType = "unexpected"
+			@RequestParser.parse @validRequest, @callback
+			@data = @callback.args[0][1]
+
+		it "should return an error", ->
+			@callback.calledWith("syncType attribute should be one of: full, incremental")
+				.should.equal true
diff --git a/test/unit/coffee/ResourceWriterTests.coffee b/test/unit/coffee/ResourceWriterTests.coffee
index fd1ae30..0804438 100644
--- a/test/unit/coffee/ResourceWriterTests.coffee
+++ b/test/unit/coffee/ResourceWriterTests.coffee
@@ -7,7 +7,11 @@ path = require "path"
 describe "ResourceWriter", ->
 	beforeEach ->
 		@ResourceWriter = SandboxedModule.require modulePath, requires:
-			"fs": @fs = { mkdir: sinon.stub().callsArg(1) }
+			"fs": @fs =
+				mkdir: sinon.stub().callsArg(1)
+				unlink: sinon.stub().callsArg(1)
+			"./ResourceListManager": @ResourceListManager = {}
+			"./ResourceStateManager": @ResourceStateManager = {}
 			"wrench": @wrench = {}
 			"./UrlCache" : @UrlCache = {}
 			"mkdirp" : @mkdirp = sinon.stub().callsArg(1)
@@ -20,7 +24,7 @@ describe "ResourceWriter", ->
 		@basePath = "/path/to/write/files/to"
 		@callback = sinon.stub()
 
-	describe "syncResourcesToDisk", ->
+	describe "syncResourcesToDisk on a full request", ->
 		beforeEach ->
 			@resources = [
 				"resource-1-mock"
@@ -29,7 +33,62 @@ describe "ResourceWriter", ->
 			]
 			@ResourceWriter._writeResourceToDisk = sinon.stub().callsArg(3)
 			@ResourceWriter._removeExtraneousFiles = sinon.stub().callsArg(2)
-			@ResourceWriter.syncResourcesToDisk(@project_id, @resources, @basePath, @callback)
+			@ResourceStateManager.checkProjectStateHashMatches = sinon.stub().callsArg(2)
+			@ResourceStateManager.saveProjectStateHash = sinon.stub().callsArg(2)
+			@ResourceListManager.saveResourceList = sinon.stub().callsArg(2)
+			@ResourceListManager.loadResourceList = sinon.stub().callsArg(1)
+			@ResourceWriter.syncResourcesToDisk({
+				project_id: @project_id
+				syncState: @syncState = "0123456789abcdef"
+				resources: @resources
+			}, @basePath, @callback)
+
+		it "should remove old files", ->
+			@ResourceWriter._removeExtraneousFiles
+				.calledWith(@resources, @basePath)
+				.should.equal true
+
+		it "should write each resource to disk", ->
+			for resource in @resources
+				@ResourceWriter._writeResourceToDisk
+					.calledWith(@project_id, resource, @basePath)
+					.should.equal true
+
+		it "should store the sync state", ->
+			@ResourceStateManager.saveProjectStateHash
+				.calledWith(@syncState, @basePath)
+				.should.equal true
+
+		it "should save the resource list", ->
+			@ResourceListManager.saveResourceList
+				.calledWith(@resources, @basePath)
+				.should.equal true
+
+		it "should call the callback", ->
+			@callback.called.should.equal true
+
+	describe "syncResourcesToDisk on an incremental update", ->
+		beforeEach ->
+			@resources = [
+				"resource-1-mock"
+			]
+			@ResourceWriter._writeResourceToDisk = sinon.stub().callsArg(3)
+			@ResourceWriter._removeExtraneousFiles = sinon.stub().callsArg(2)
+			@ResourceStateManager.checkProjectStateHashMatches = sinon.stub().callsArg(2)
+			@ResourceStateManager.saveProjectStateHash = sinon.stub().callsArg(2)
+			@ResourceListManager.saveResourceList = sinon.stub().callsArg(2)
+			@ResourceListManager.loadResourceList = sinon.stub().callsArgWith(1, null, @resources)
+			@ResourceWriter.syncResourcesToDisk({
+				project_id: @project_id,
+				syncType: "incremental",
+				syncState: @syncState = "1234567890abcdef",
+				resources: @resources
+			}, @basePath, @callback)
+
+		it "should check the sync state matches", ->
+			@ResourceStateManager.checkProjectStateHashMatches
+				.calledWith(@syncState, @basePath)
+				.should.equal true
 
 		it "should remove old files", ->
 			@ResourceWriter._removeExtraneousFiles
@@ -45,6 +104,28 @@ describe "ResourceWriter", ->
 		it "should call the callback", ->
 			@callback.called.should.equal true
 
+	describe "syncResourcesToDisk on an incremental update when the state does not match", ->
+		beforeEach ->
+			@resources = [
+				"resource-1-mock"
+			]
+			@ResourceStateManager.checkProjectStateHashMatches = sinon.stub().callsArgWith(2, @error = new Error())
+			@ResourceWriter.syncResourcesToDisk({
+				project_id: @project_id,
+				syncType: "incremental",
+				syncState: @syncState = "1234567890abcdef",
+				resources: @resources
+			}, @basePath, @callback)
+
+		it "should check whether the sync state matches", ->
+			@ResourceStateManager.checkProjectStateHashMatches
+				.calledWith(@syncState, @basePath)
+				.should.equal true
+
+		it "should call the callback with an error", ->
+			@callback.calledWith(@error).should.equal true
+
+
 	describe "_removeExtraneousFiles", ->
 		beforeEach ->
 			@output_files = [{