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

lthames
lthames used Ask the Experts™
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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!
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Most Valuable Expert 2011
Commented:
Have you seen this? https://www.jetbrains.com/phpstorm/help/configuring-line-separators.html

I think this bit might be relevant?
To change line separator for a file or directory, selected in the project view

    Select a file or directory in the Project tool window.

    Note that if a directory is selected, the line ending style applies to all nested files recursively.
    Choose File | Line Separatorson the main menu, and then select the desired line ending style from the sub-menu.

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