Just put directly the eol to unix style for your .sh files.
Even if your building environment is on windows, you are using a cygwin environment right? Anyway, windows command interpreter cmd.exe can not understand shell scripts in the first place, so you don't have to worry about windows carriage return.
Optionally, you can configure the way Git manages line endings on a
per-repository basis by configuring a special .gitattributes file.
This file is committed into the repository and overrides an
individual's core.autocrlf setting, ensuring consistent behavior for
all users, regardless of their Git settings. The advantage of a
.gitattributes file is that your line configurations are associated
with your repository. You don't need to worry about whether or not
collaborators have the same line ending settings that you do.
The .gitattributes file must be created in the root of the repository
and committed like any other file.
A .gitattributes file looks like a table with two columns:
On the left is the file name for Git to match. On the right is the
line ending configuration that Git should use for those files.
Here's an example .gitattributes file. You can use it as a template
for your repositories:
# Set the default behavior, in case people don't have core.autocrlf set.
* text=auto
# Explicitly declare text files you want to always be normalized and converted
# to native line endings on checkout.
*.c text
*.h text
# Declare files that will always have CRLF line endings on checkout.
*.sln text eol=crlf
# Denote all files that are truly binary and should not be modified.
*.png binary
*.jpg binary
You'll notice that files are matched--*.c, *.sln, *.png--, separated
by a space, then given a setting--text, text eol=crlf, binary. We'll
go over some possible settings below.
text=auto Git will handle the files in whatever way it thinks is best.
This is a good default option. text eol=crlf Git will always convert
line endings to CRLF on checkout. You should use this for files that
must keep CRLF endings, even on OSX or Linux. text eol=lf Git will
always convert line endings to LF on checkout. You should use this for
files that must keep LF endings, even on Windows. binary Git will
understand that the files specified are not text, and it should not
try to change them. The binary setting is also an alias for -text
-diff.
Source: https://help.github.com/articles/dealing-with-line-endings/
Additional readings: How to change line-ending settings
