Git showing changed files, but not on command line

Hello David,

What is shown in the Changes toolwindow?

Shows the default node of 1600 files..

however git from the command line says: "Nothing to commit (working directory clean)"

which usually tells me there are no changes..

Pics attached

As a note, I've tried refreshing several different ways inside of Idea.. they always seem to be marked as changed..

Please check that your Git root is correctly set up in Settings -> Version Control

Do you have any Git repositories above the project dir?

Git root is setup to be "current directory" ie: a .

There is might be a git repo somewhere higher.. although not in the project..

ie: the project directory is c:\users\dave\programming\web\Project <- git root as well

there are definately other git roots in the web directory, in thier own subdirs..

there might be some in my user dir..

but according to the Idea project.. there's nothing higher.. if you know what I mean..

1. Please check if all the changes displayed in the Changes View belong to this project, or there are others (to make it simplier, you may enable grouping changes by folder by pressing the button in the Changes View toolbar).

2. Make a screenshot of Settings -> Version Control.

3. Try to call git status from the directory above the project dir (i.e. from c:\users\dave\programming\web). Does it display anything?

Here you go.. all the pictures
1) They seem to all be where they should be
2) Attached
3) The error which I expected, as it's not a git repo :) (pic attached)

It's probably worth mentioning that I don't have this problem on EVERY project, just ones that I checkout ont he command line.. ie:  I started the project using sublime text 2 ( a text editor) .. but it got a little complex so I created a project in idea and started using that..

now I have no doubt if I checked this out from within IDEA it would be fine.. and here's the kicker.. not ALL files show changed.. but most do.. is there  a cache file that idea uses that I can invalidate or something that might have the sync status?!

Just grasping here..

1. Is it 100 % reproducible that the bug happens, when you start developing outside and then create an IDEA project after it? I.e. does the bug happen for ALL your projects that were started in the command line?

2. Please attach idea.log. (Help -> Reveal Log in Explorer)

3. We don't cache the statuses. You can press the Refresh button in the Changes View, and it will call git status on the whole repository. But I doubt that it can help, since we call refresh anyway in several cases such as project load,etc.

4. Please check the Git executable registered in IDEA: is it the same as you use from the command line?

5. Please invoke show diff on a file which is shown as modified in the Changes View. Can you say something about these differences?
For exampe, something like "the version at the left is not the current HEAD, but an old revision two weeks ago" (you may also check the revision hash above the left diff panel).

That was it..

I found that I was using a different version of git (c:\msysgit) where as on the command line I use Cygwin..

Changed it.. updated and n ow they are fine..

Awesome .. thanks for all the help

Ah, probably that happened because of different CRLF settings in different git installations.
If true, than all the modifications should be just line endings.