     files = fs.listSync(rootPath)
     files = files.filter (file) ->
       return !(utilities.getFilenameExt(file).toLowerCase() in settings.notSourceExtensions)
+
+    process.chdir rootPath
+    files = (path.relative(rootPath, file) for file in files)
 
     workspace = atom.workspaceView
     @compileCloudPromise = @spark.compileCode files

  # Flash core via the cloud
  flashCloud: (firmware=null) -> @coreRequired => @projectRequired =>
    fs ?= require 'fs-plus'
    utilities ?= require './vendor/utilities'

    rootPath = atom.project.getPath()


      if !firmware
        firmware = files[0]

      process.chdir rootPath
      firmware = path.relative rootPath, firmware

      @statusView.setStatus 'Flashing via the cloud...'

