I can't tell if you are talking about files created during the build or files 
checked out for the build but if it is files checked out for the build perhaps 
your git line endings are set wrong.  If the git repo is for windows and git 
then you need it set to use linux line endings.  Check out this page:
https://help.github.com/articles/dealing-with-line-endings

Will
________________________________
From: jenkinsci-users@googlegroups.com [jenkinsci-users@googlegroups.com] on 
behalf of David Brossard [dbross...@gmail.com]
Sent: Wednesday, March 27, 2013 1:24 PM
To: jenkinsci-users@googlegroups.com
Subject: Jenkins, Git, Windows and Line Feeds

All,
This has been frustrating me for a while. I need to both build Windows code and 
publish Linux code during a single build. The only way I've been able to get 
this to build is to run completely on a Windows slave. If I try to run on a 
linux slave as well it always complains that MSBuild cannot be found. So I 
force it onto my windows slave and use GIT to check out the code, build with 
MSBuild, then push out to both Windows and Linux without error.
Now my issue is that the code pushed to my Linux box has been converted to 
Windows' CR/LF method so none of my executables work on Linux. Short of doing a 
dos2unix on every single file I push out, is there a way to fix this? I tried 
adding "*   text=binary" to my gitattributes but to no avail. I think it may be 
ignoring that attributes file because jgit is used instead of git?
Any and all help greatly appreciated.
Thanks

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