In phpStorm, how can I ignore line separator differences when syncing deployed files on a linux server with files on my windows PC?

I use phpStorm to develop on Magento sites.  When I have downloaded code from Linux to my Windows 8 pc and then later try to sync the 2 to find and update changes made to the remote code,  every file comes up as changed but the listed changes say 'Contents have differences in only line separators'.    Here is a screenshot:  http://screencast.com/t/6jf562rYsX

Can I get phpStorm to ignore these differences when syncing?  Or can I get phpStorm  to leave the line separators alone when downloading?  

I've searched their help and found similar suggestions but nothing seemed to be exactly what I am experiencing (at least that I can tell).  I am new to phpStorm and not very Linux savy.

Thanks for any guidance you can give!