agent: fixed "modified" files after clone.

Due to CR/LF issue some files were reported as "modified" even after
new clone or hard reset. Recommited the files with the right line-
ending.

Change-Id: I147b60f91335e18d786f79e3ab5d3799c1b18ab8
Signed-off-by: Gal Hammer <ghammer@redhat.com>