git status difference between git clients

Question

For the last few years I'm using SourceTree as git client. Yesterday I tried last version of Github Desktop (version Infinite Lop (214)). It’s better than all other version that I tried before. Still not better than SourceTree, but anyway I like it :) And I decide to use instead of SourceTree for a while.

But today I open another project and I was surprise with some file statuses. It’s shows that there are over 90 uncommitted changes :

But in fact I only change few files. How it’s happen. For to be sure, I check in terminal for same project with :

=> git status

but surprise surprise, it shows same results on OSX's git version too :

On branch SomeBranchNameOfProject
Changes not staged for commit:
  (use "git add/rm <file>..." to update what will be committed)
  (use "git checkout -- <file>..." to discard changes in working directory)

    modified:   Podfile
    typechange: Pods/Headers/Public/AFNetworking/AFHTTPRequestOperation.h
    typechange: Pods/Headers/Public/AFNetworking/AFHTTPRequestOperationManager.h
    typechange: Pods/Headers/Public/AFNetworking/AFHTTPSessionManager.h
    typechange: Pods/Headers/Public/AFNetworking/AFNetworkActivityIndicatorManager.h
    typechange: Pods/Headers/Public/AFNetworking/AFNetworkReachabilityManager.h
    typechange: Pods/Headers/Public/AFNetworking/AFNetworking.h
    typechange: Pods/Headers/Public/AFNetworking/AFSecurityPolicy.h
    typechange: Pods/Headers/Public/AFNetworking/AFURLConnectionOperation.h
    typechange: Pods/Headers/Public/AFNetworking/AFURLRequestSerialization.h
    typechange: Pods/Headers/Public/AFNetworking/AFURLResponseSerialization.h
    typechange: Pods/Headers/Public/AFNetworking/AFURLSessionManager.h
    typechange: Pods/Headers/Public/AFNetworking/UIActivityIndicatorView+AFNetworking.h
    typechange: Pods/Headers/Public/AFNetworking/UIAlertView+AFNetworking.h
    typechange: Pods/Headers/Public/AFNetworking/UIButton+AFNetworking.h
    typechange: Pods/Headers/Public/AFNetworking/UIImageView+AFNetworking.h
    typechange: Pods/Headers/Public/AFNetworking/UIKit+AFNetworking.h
    typechange: Pods/Headers/Public/AFNetworking/UIProgressView+AFNetworking.h
    typechange: Pods/Headers/Public/AFNetworking/UIRefreshControl+AFNetworking.h
    typechange: Pods/Headers/Public/AFNetworking/UIWebView+AFNetworking.h
    typechange: Pods/Headers/Public/BPXLUUIDHandler/BPXLUUIDHandler.h
    typechange: Pods/Headers/Public/CocoaLumberjack/CocoaLumberjack.h
    typechange: Pods/Headers/Public/CocoaLumberjack/DDASLLogCapture.h
    typechange: Pods/Headers/Public/CocoaLumberjack/DDASLLogger.h
    typechange: Pods/Headers/Public/CocoaLumberjack/DDAbstractDatabaseLogger.h
    typechange: Pods/Headers/Public/CocoaLumberjack/DDAssertMacros.h
    typechange: Pods/Headers/Public/CocoaLumberjack/DDContextFilterLogFormatter.h
    typechange: Pods/Headers/Public/CocoaLumberjack/DDDispatchQueueLogFormatter.h
    typechange: Pods/Headers/Public/CocoaLumberjack/DDFileLogger.h
    typechange: Pods/Headers/Public/CocoaLumberjack/DDLegacyMacros.h
    typechange: Pods/Headers/Public/CocoaLumberjack/DDLog+LOGV.h
    typechange: Pods/Headers/Public/CocoaLumberjack/DDLog.h
    typechange: Pods/Headers/Public/CocoaLumberjack/DDLogMacros.h
    typechange: Pods/Headers/Public/CocoaLumberjack/DDMultiFormatter.h
    typechange: Pods/Headers/Public/CocoaLumberjack/DDTTYLogger.h
    typechange: Pods/Headers/Public/MBProgressHUD/MBProgressHUD.h
    typechange: Pods/Headers/Public/MMDrawerController/MMDrawerBarButtonItem.h
    typechange: Pods/Headers/Public/MMDrawerController/MMDrawerController+Subclass.h
    typechange: Pods/Headers/Public/MMDrawerController/MMDrawerController.h
    typechange: Pods/Headers/Public/MMDrawerController/MMDrawerVisualState.h
    typechange: Pods/Headers/Public/MMDrawerController/UIViewController+MMDrawerController.h
    typechange: Pods/Headers/Public/Mantle/MTLJSONAdapter.h
    typechange: Pods/Headers/Public/Mantle/MTLModel+NSCoding.h
    typechange: Pods/Headers/Public/Mantle/MTLModel.h
    typechange: Pods/Headers/Public/Mantle/MTLReflection.h
    typechange: Pods/Headers/Public/Mantle/MTLTransformerErrorHandling.h
    typechange: Pods/Headers/Public/Mantle/MTLValueTransformer.h
    typechange: Pods/Headers/Public/Mantle/Mantle.h
    typechange: Pods/Headers/Public/Mantle/NSArray+MTLManipulationAdditions.h
    typechange: Pods/Headers/Public/Mantle/NSDictionary+MTLJSONKeyPath.h
    typechange: Pods/Headers/Public/Mantle/NSDictionary+MTLManipulationAdditions.h
    typechange: Pods/Headers/Public/Mantle/NSDictionary+MTLMappingAdditions.h
    typechange: Pods/Headers/Public/Mantle/NSError+MTLModelException.h
    typechange: Pods/Headers/Public/Mantle/NSObject+MTLComparisonAdditions.h
    typechange: Pods/Headers/Public/Mantle/NSValueTransformer+MTLInversionAdditions.h
    typechange: Pods/Headers/Public/Mantle/NSValueTransformer+MTLPredefinedTransformerAdditions.h
    typechange: Pods/Headers/Public/Reachability/Reachability.h
    typechange: Pods/Headers/Public/SDWebImage/NSData+ImageContentType.h
    typechange: Pods/Headers/Public/SDWebImage/SDImageCache.h
    typechange: Pods/Headers/Public/SDWebImage/SDWebImageCompat.h
    typechange: Pods/Headers/Public/SDWebImage/SDWebImageDecoder.h
    typechange: Pods/Headers/Public/SDWebImage/SDWebImageDownloader.h
    typechange: Pods/Headers/Public/SDWebImage/SDWebImageDownloaderOperation.h
    typechange: Pods/Headers/Public/SDWebImage/SDWebImageManager.h
    typechange: Pods/Headers/Public/SDWebImage/SDWebImageOperation.h
    typechange: Pods/Headers/Public/SDWebImage/SDWebImagePrefetcher.h
    typechange: Pods/Headers/Public/SDWebImage/UIButton+WebCache.h
    typechange: Pods/Headers/Public/SDWebImage/UIImage+GIF.h
    typechange: Pods/Headers/Public/SDWebImage/UIImage+MultiFormat.h
    typechange: Pods/Headers/Public/SDWebImage/UIImageView+HighlightedWebCache.h
    typechange: Pods/Headers/Public/SDWebImage/UIImageView+WebCache.h
    typechange: Pods/Headers/Public/SDWebImage/UIView+WebCacheOperation.h

in fact SourceTree doesn’t show that files with “Changes not staged for commit” warning!

I know that source tree uses own embeded Git, and I could change that in preferences :

That means, SourceTree could show same "not staged files" too probably...

My question is, how could I use Github Desktop with same experience like how I use SourceTree? And what is wrong with my CocoaPods files. Or if I understand something wrong, please guide me to fix this behaviour.

Answer 1

After asking my question I update my OSX to version 10.11.1 (15B42) and XCode to Version 7.1 (7B91b). But things get worse XCode start to show question mark for all files in workspace (means : file untracked by source control). That moment I realise something wrong with my .git directory in my workspace. I open the terminal and enter inside of .git directory. And I check old copy of my project from my backup directory (If you have a backup you are lucky...). It was different than before. I know that SourceTree was adding sourcetreeconfig directory in my .git directory and there was more than this. I understand that Github Desktop add that directories and everybody (all clients) effect each other except lovely sweet sweet SourceTree! I want to say thank you for team and Atlassian.

Solution : I remove other directories created from Github Desktop and everything working like a charm now.

So my adverture with Github Desktop paused by now. But after few days I’ll try again but only work with Github Desktop this time. Why? Because I love it :)

Thank you for your comment @torek.