Diff between 2 projects generated with ionic (rc-1) cli. The diff file is generated via diff comparing failed-project to success-project.

pbxproj-diff.txt

8d7
< 
15a15,21
> 		7AA484D8671B4F4FAD2BEFAA /* CDVLogger.m in Sources */ = {isa = PBXBuildFile; fileRef = 7F92630E181141039AA090FB /* CDVLogger.m */; };
> 		C09B4047D1DF43B88E365E5C /* CDVDevice.m in Sources */ = {isa = PBXBuildFile; fileRef = E64DC7260FBA48608D8FD2FE /* CDVDevice.m */; };
> 		E3ADD04642B74603A7EE2AB0 /* NativeStorage.m in Sources */ = {isa = PBXBuildFile; fileRef = AB9742C2704E405482736609 /* NativeStorage.m */; };
> 		FBD7F35D70D548328D3BC273 /* CDVSplashScreen.m in Sources */ = {isa = PBXBuildFile; fileRef = 2991DB23B4884D6792BDC50F /* CDVSplashScreen.m */; };
> 		4B80DF741B8148C1AC120FEC /* CDVViewController+SplashScreen.m in Sources */ = {isa = PBXBuildFile; fileRef = 5276D82FEB1341EB88B0BD64 /* CDVViewController+SplashScreen.m */; };
> 		BC93ABE0255D4DB28AECFD03 /* CDVStatusBar.m in Sources */ = {isa = PBXBuildFile; fileRef = 14593FC73F464F68B07F8DC4 /* CDVStatusBar.m */; };
> 		8F517527A4C446EB947AE5B2 /* IonicKeyboard.m in Sources */ = {isa = PBXBuildFile; fileRef = C406194DB33C4C6799308019 /* IonicKeyboard.m */; };
54a61,74
> 		7F92630E181141039AA090FB /* CDVLogger.m */ = {isa = PBXFileReference; name = "CDVLogger.m"; path = "cordova-plugin-console/CDVLogger.m"; sourceTree = "<group>"; fileEncoding = 4; lastKnownFileType = sourcecode.c.objc; explicitFileType = undefined; includeInIndex = 0; };
> 		463C1589AA4B4DAEB25C091E /* CDVLogger.h */ = {isa = PBXFileReference; name = "CDVLogger.h"; path = "cordova-plugin-console/CDVLogger.h"; sourceTree = "<group>"; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; explicitFileType = undefined; includeInIndex = 0; };
> 		E64DC7260FBA48608D8FD2FE /* CDVDevice.m */ = {isa = PBXFileReference; name = "CDVDevice.m"; path = "cordova-plugin-device/CDVDevice.m"; sourceTree = "<group>"; fileEncoding = 4; lastKnownFileType = sourcecode.c.objc; explicitFileType = undefined; includeInIndex = 0; };
> 		A6660D0B4F0D45B5997EB189 /* CDVDevice.h */ = {isa = PBXFileReference; name = "CDVDevice.h"; path = "cordova-plugin-device/CDVDevice.h"; sourceTree = "<group>"; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; explicitFileType = undefined; includeInIndex = 0; };
> 		AB9742C2704E405482736609 /* NativeStorage.m */ = {isa = PBXFileReference; name = "NativeStorage.m"; path = "cordova-plugin-nativestorage/NativeStorage.m"; sourceTree = "<group>"; fileEncoding = 4; lastKnownFileType = sourcecode.c.objc; explicitFileType = undefined; includeInIndex = 0; };
> 		60B9D2936BF247BE9005DF99 /* NativeStorage.h */ = {isa = PBXFileReference; name = "NativeStorage.h"; path = "cordova-plugin-nativestorage/NativeStorage.h"; sourceTree = "<group>"; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; explicitFileType = undefined; includeInIndex = 0; };
> 		2991DB23B4884D6792BDC50F /* CDVSplashScreen.m */ = {isa = PBXFileReference; name = "CDVSplashScreen.m"; path = "cordova-plugin-splashscreen/CDVSplashScreen.m"; sourceTree = "<group>"; fileEncoding = 4; lastKnownFileType = sourcecode.c.objc; explicitFileType = undefined; includeInIndex = 0; };
> 		5276D82FEB1341EB88B0BD64 /* CDVViewController+SplashScreen.m */ = {isa = PBXFileReference; name = "CDVViewController+SplashScreen.m"; path = "cordova-plugin-splashscreen/CDVViewController+SplashScreen.m"; sourceTree = "<group>"; fileEncoding = 4; lastKnownFileType = sourcecode.c.objc; explicitFileType = undefined; includeInIndex = 0; };
> 		A8613795AF9349ABB4BDF728 /* CDVSplashScreen.h */ = {isa = PBXFileReference; name = "CDVSplashScreen.h"; path = "cordova-plugin-splashscreen/CDVSplashScreen.h"; sourceTree = "<group>"; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; explicitFileType = undefined; includeInIndex = 0; };
> 		9D4EFAEDD91F4CA2BFC8F3D9 /* CDVViewController+SplashScreen.h */ = {isa = PBXFileReference; name = "CDVViewController+SplashScreen.h"; path = "cordova-plugin-splashscreen/CDVViewController+SplashScreen.h"; sourceTree = "<group>"; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; explicitFileType = undefined; includeInIndex = 0; };
> 		14593FC73F464F68B07F8DC4 /* CDVStatusBar.m */ = {isa = PBXFileReference; name = "CDVStatusBar.m"; path = "cordova-plugin-statusbar/CDVStatusBar.m"; sourceTree = "<group>"; fileEncoding = 4; lastKnownFileType = sourcecode.c.objc; explicitFileType = undefined; includeInIndex = 0; };
> 		B981AA00E7BD408490F3CD10 /* CDVStatusBar.h */ = {isa = PBXFileReference; name = "CDVStatusBar.h"; path = "cordova-plugin-statusbar/CDVStatusBar.h"; sourceTree = "<group>"; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; explicitFileType = undefined; includeInIndex = 0; };
> 		C406194DB33C4C6799308019 /* IonicKeyboard.m */ = {isa = PBXFileReference; name = "IonicKeyboard.m"; path = "ionic-plugin-keyboard/IonicKeyboard.m"; sourceTree = "<group>"; fileEncoding = 4; lastKnownFileType = sourcecode.c.objc; explicitFileType = undefined; includeInIndex = 0; };
> 		456916AA983440EFAB3210EB /* IonicKeyboard.h */ = {isa = PBXFileReference; name = "IonicKeyboard.h"; path = "ionic-plugin-keyboard/IonicKeyboard.h"; sourceTree = "<group>"; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; explicitFileType = undefined; includeInIndex = 0; };
156a177,190
> 				7F92630E181141039AA090FB /* CDVLogger.m */,
> 				463C1589AA4B4DAEB25C091E /* CDVLogger.h */,
> 				E64DC7260FBA48608D8FD2FE /* CDVDevice.m */,
> 				A6660D0B4F0D45B5997EB189 /* CDVDevice.h */,
> 				AB9742C2704E405482736609 /* NativeStorage.m */,
> 				60B9D2936BF247BE9005DF99 /* NativeStorage.h */,
> 				2991DB23B4884D6792BDC50F /* CDVSplashScreen.m */,
> 				5276D82FEB1341EB88B0BD64 /* CDVViewController+SplashScreen.m */,
> 				A8613795AF9349ABB4BDF728 /* CDVSplashScreen.h */,
> 				9D4EFAEDD91F4CA2BFC8F3D9 /* CDVViewController+SplashScreen.h */,
> 				14593FC73F464F68B07F8DC4 /* CDVStatusBar.m */,
> 				B981AA00E7BD408490F3CD10 /* CDVStatusBar.h */,
> 				C406194DB33C4C6799308019 /* IonicKeyboard.m */,
> 				456916AA983440EFAB3210EB /* IonicKeyboard.h */,
199c233
< 				LastUpgradeCheck = 0510;
---
> 				LastUpgradeCheck = 510;
275a310,316
> 				7AA484D8671B4F4FAD2BEFAA /* CDVLogger.m in Sources */,
> 				C09B4047D1DF43B88E365E5C /* CDVDevice.m in Sources */,
> 				E3ADD04642B74603A7EE2AB0 /* NativeStorage.m in Sources */,
> 				FBD7F35D70D548328D3BC273 /* CDVSplashScreen.m in Sources */,
> 				4B80DF741B8148C1AC120FEC /* CDVViewController+SplashScreen.m in Sources */,
> 				BC93ABE0255D4DB28AECFD03 /* CDVStatusBar.m in Sources */,
> 				8F517527A4C446EB947AE5B2 /* IonicKeyboard.m in Sources */,

steps-reproduce.txt

Steps to reproduce the diff as shown can be done as follows.
- create a normal ionic project via ionic start <project> --v2 (only test via ionic 2)
- make sure plugins/ios.json is removed
- normally ios platform will be added, if not execute `ionic platform add ios`
- `ionic build`
- (up to this steps: we got a success project) Then go to XCode project generated in platforms/ios, build the project and deploy on device. You will see no error about Plugin no found or similar message.
- Make some changes to .ts file.
- `ionic platform update ios`
- `ionic build`
- (up to this steps: we got a failed project) Go to Xcode project, build and deploy on device. You will see Plugins not found error all over the place in debugging console.

Related issue and discussion can be found at this thread https://forum.ionicframework.com/t/plugins-does-not-exist/2980/4