Resolve the to real paths when calculating relative path for file upload

[mmolnar]

This will resolve #181

[mmolnar]

Also note that I am not a NodeJS developer, so feel free to rewrite the fix as you see fit.

[mmolnar]

To elaborate on the problem:
The variable @ProjectPath in ScpTransport.coffee contains path to the Project, this path contains a symlink. For example:
@ProjectPath = '/home/user/projects/atom/amazing-project'

But the projects directory in /home/user/ is a symlink to /media/disk/projects .

When uploading the file using 'Upload File' command or when using uploadOnSave the following path is passed:
localFilePath = '/media/disk/projects/atom/amazing-project/upload.file'
But when using 'Upload Folder' command, the following path is passed:
localFilePath = '/home/user/projects/atom/amazing-project/upload.file'

This is causing the value of targetFilePath to contain wrong relative path.