Why do I get different results in git bash (msysgit) and git in cygwin?

I alyways used the git bash but now I have to change to cygwin because I need wget and other things, so I thought I could use the builtin git as well since it is newer.

The git bash is version 1.9.4-preview, the one in cygwin is version 2.1.4. I have a cloned repo I worked with using the git bash. I commited and pushed everything and I'm on the develop branch. When I use "git status" I get this:

On branch develop
Your branch is up-to-date with 'origin/develop'.

nothing to commit, working directory clean

In cygwin I get this part

On branch develop
Your branch is up-to-date with 'origin/develop'.

But then I get a list of hundreds of files that are not staged for commit. Why do I get different results? I'm in the same directory in the same repo, the results should be the same.

Solution

It’s most likely due to differences between the two Git configurations. Git uses a number of configuration settings to tell it how to behave such as how to treat differences between DOS and Unix-style line endings. These include:

core.autocrlf
core.ignorecase
core.eol

See git config --help for more info on these and other configuration options.

You should run the following commands on both systems and compare the configuration settings:

git config --system --list
git config --global --list

Note that the global settings take precedence over the system settings. The system settings are set for every user on the system (/etc/gitconfig in Cygwin) while the global settings are for only your user account (~/.gitconfig on Cygwin) and apply to all your repositories.

Also: you can also run git config --local --list to see the configuration settings which are local to the repository – but these will be the same on both Cygwin and MSys Git.