command in project.scan needs to resolve to the bin, not the lib file

This is because nak was changed to also be run as a regular Node script, not just an executable

src/app/project.coffee

@@ -1,3 +1,4 @@
+Path = require 'path'
 fsUtils = require 'fs-utils'
 _ = require 'underscore'
 $ = require 'jquery'
@@ -274,7 +275,7 @@ class Project
         readPath(line) if state is 'readingPath'
         readLine(line) if state is 'readingLines'
 
-    command = require.resolve('nak')
+    command = Path.resolve(require.resolve('nak'), '../../bin/nak')
     args = ['--hidden', '--ackmate', regex.source, @getPath()]
     ignoredNames = config.get('core.ignoredNames') ? []
     args.unshift('--ignore', ignoredNames.join(',')) if ignoredNames.length > 0