My anwer from here: https://forums.developer.apple.com/thread/17063?sr=stream&ru=18990
Possible solution:
After struggling with this for three days now, we do have a solution that works for us and hopefully works for some of you as well:
It seems like that creating the .ipa your self e.g. through a continuous integration server is NOT possible anymore as it then contains the wrong swift and watch kit support files. So the first thing you should try is:
Archive and upload your app through Xcode 7 GM.
This, however, didn't work for as either as the 'Upload to App Store...' button was grayed out because Xcode marked the created archive as 'Generic Xcode Archive' instead of 'iOS App Archive'.
It turns out, this happens when you have cocoapods link a framework to a watchOS 2 application.
To fix this we had to digg a little bit deeper into the archive: Open the archive in the Finder, right click on it and chose 'Show package contents'. Open the 'Info.plist' of the archive in a text editor and add the following:
<key>ApplicationProperties</key>
<dict>
<key>ApplicationPath</key>
<string>Applications/<<APP_NAME>>.app</string>
<key>CFBundleIdentifier</key>
<string><<BUNDLE_IDENTIFIER>></string>
<key>CFBundleShortVersionString</key>
<string><<YOUR_MARKETING_NUMBER>></string>
<key>CFBundleVersion</key>
<string><<YOUR_BUILD_NUMBER>></string>
<key>SigningIdentity</key>
<string>iPhone Distribution: <<CERTIFICATE_NAME>> (<<CERTIFICATE_ID>>)</string>
</dict>
If you have an old, working archive, you can copy the values from there and simply change the marketing version and the build number.
After closing Xcode and restarting it, the archive was shown as 'iOS App Archive' and we could successfully upload the binary to the app store through Xcode.
Note: I filled the ipa generation issue under rdar://22683061 and the cocoapods releated archive building issue under rdar://22682898