Well, I found this problem under windows when I was trying to check my project to TFS.

I was bumping my head to find a solution. I tried this and it just works!!
Thank you so much.

Some questions:
If I install another module after I run flatten-deps, can I run it again to flatten the new module?
Does this work with in all situations, or could it break my project?

When trying to flatten a project:

fs.js:554
return binding.rename(pathModule._makeLong(oldPath),
^
Error: EPERM, operation not permitted 'D:\TFS\AppRoot\App\node_modules\adm-zip'
at Object.fs.renameSync (fs.js:554:18)
at moveIfPossible (C:\Users\myuser\AppData\Roaming\npm\node_modules\flatten-deps\lib\flatten.coffee:54:10)
at run (C:\Users\hats\AppData\Roaming\npm\node_modules\flatten-deps\lib\flatten.coffee:69:9)
at Object. (C:\Users\hats\AppData\Roaming\npm\node_modules\flatten-deps\bin\flatten-deps:3:25)
at Module._compile (module.js:456:26)
at Object.Module._extensions..js (module.js:474:10)
at Module.load (module.js:356:32)
at Function.Module._load (module.js:312:12)
at Function.Module.runMain (module.js:497:10)
at startup (node.js:119:16)
at node.js:906:3