I had the same problem and figured out how to remove the unwanted branch in this environment: XCODE 7.3 (7D175) and using CocoaPods generating the .xcworkspace file.
, :
1. MyApplication.xcworkspace.
2. TextWrangler ( ).
3. : "xcshareddata" "xcuserdata". Unfold 'xcshareddata'.
4. MyApplication.xcsmblueprint.
, , .
"DVTSourceControlWorkspaceBlueprintIdentifierKey", , , .
.
XCODE, "Source Control".
@ :
.xcscmblueprint "DVTSourceControlWorkspaceBlueprintWorkingCopyPathsKey" ( 12). , 3 .
, 3 , (?).
, "DVTSourceControlWorkspaceBlueprintRemoteRepositoriesKey" ( 20), 3 .
, , , ( "DVTSourceControlWorkspaceBlueprintRemoteRepositoryURLKey" ).
, , , "DVTSourceControlWorkspaceBlueprintWorkingCopyStatesKey" ( 6) 2 , 2 .
, 3 "DVTSourceControlWorkspaceBlueprintWorkingCopyPathsKey" ( 12).
, : 2 "DVTSourceControlWorkspaceBlueprintRemoteRepositoriesKey" ( 20).
.: )