1. Никакого project.xcworkspace в проекте нет.
2. Workspace _не_ перегенеривается:

```
$ git clone git://github.com/eploko/yandexmapkit-ios.git
Cloning into 'yandexmapkit-ios'...
remote: Counting objects: 472, done.
remote: Compressing objects: 100% (206/206), done.
remote: Total 472 (delta 341), reused 381 (delta 250)
Receiving objects: 100% (472/472), 146.91 KiB, done.
Resolving deltas: 100% (341/341), done.
$ cd yandexmapkit-ios/
$ git co dependencies-as-cocoapods
Branch dependencies-as-cocoapods set up to track remote branch dependencies-as-cocoapods from origin.
Switched to a new branch 'dependencies-as-cocoapods'
$ pod install
Resolving dependencies of `./Podfile'
Resolving dependencies for target `default' (iOS 5.0)
Downloading dependencies
Installing YandexMapKit (1.0.4)
[!] Appledoc encountered an error (exitstatus: 250), an update might be available to solve the issue.
Generating support files

$ git status
# On branch dependencies-as-cocoapods
nothing to commit, working directory clean
$ 
```