diff returning entire file for identical files

I've got a website that has a git repo. I cloned the repo so that I could develop in one directory and then push to the repo, and then pull in the live/prod directory (would be interested in suggestions for a better way to do this if there is one, but that's outside the scope of this question).

I did the following in the live directory to push all my latest changes:

git add .
git commit -a // added a message
git push

I then did the following in the dev directory:

git clone [email protected]:user/repo.git

I then opened two files, prod/root/test.php and dev/root/test.php, and they looked identical. However, when I did the following diff command, it outputted the entire file:

diff prod/root/test.php dev/root/test.php

I am so confused as to why diff would output the entire file if they're identical... I also tried googling this and can't find anyone else with this problem. Maybe it's a line endings issue or a character encoding issue where they look the same but they are actually different and git/bitbucket converts it when you push to their repo? That's the only thing I can think of... Either that or I'm missing something really obvious.

Here's the output:

1,3c1,3
< <?
< echo '<p>Hello world!</p>';
< ?>
---
> <?
> echo '<p>Hello world!</p>';
> ?>

This seems like a whitespace issue, in order to avoid them in the future, you can setup Git to normalize them.

Windows and UNIX system don't use same line-ending, to prevent conflict from happening based on these, you should setup you git config this way:

• Windows : git config --global core.autocrlf true
• Unix : git config --global core.autocrlf input

Next, to make sure we only commit with ideal whitespace rules, you can set this config option:

git config --global core.whitespace trailing-space,space-before-tab,indent-with-non-tab

Most likely it's line termination. Try git diff --ignore-space-at-eol. And for plain (not git) diff it's diff -b.

That usually means the line endings are different. Most diffin programs allow you to ignore differences in line endings. Does yours allow you to do so?