I had a project in Yosemite using cocoa pods workspace to open it, after I update to Sierra, only pods content are available and my files are not there under xcodeproj file in Xcode inspector
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when you install pod , you must close current fileProject "yourProgramName.xcodeproj" => after install pods will already xcode make file with extensions ".xcworkspace" you must open it .

Bassam
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yes I know and I have created pods well before these happen, and I was working with it and develop a lot of code with my workspace file, but when I update to OS X Sierra it change to the form you see in the picture, it is kind of disable within .xcworkspace file – sssaaan Sep 25 '16 at 10:01
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if you open the ".xcworkspace" try to remove pods and his attached file and and reinstall pods , because in your picture seems you open ".xcodeproj" – Bassam Sep 27 '16 at 08:10
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and you can make 1- clear to project " cmd + c " . 2- that delete it from "windows/projects" 3-build project "cmd+b" – Bassam Sep 27 '16 at 08:12
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http://stackoverflow.com/questions/5996966/xcode-4-shows-no-files-after-loading-project – Bassam Sep 27 '16 at 08:26
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how do I delete pods and reinstall again, should I delete it manually ? – sssaaan Sep 27 '16 at 08:42
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I have seen the post previously but it did not answer my question @Bassam – sssaaan Sep 27 '16 at 10:16
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delete in manually . to reinstall it from terminal make " pod init " if you also delete podfile pod install – Bassam Sep 28 '16 at 06:38
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I've done that but the problem did not solvi had probleme, actually at that time when I copied to another project I had to copy but both of copies changed after chages, do not know the if from that time – sssaaan Oct 01 '16 at 13:53
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I delete them manually and I install them again the problem solved but half of my files is not here :( – sssaaan Oct 02 '16 at 17:00