CocoaPods works well for people using containers. It is much harder to use when you develop pods or, even worse, when developing an application along with (a) the libra (y), which are all pods ... (which can depend on pods as well).
What you should know is that CocoaPods is here to resolve dependencies. Your problem seems to me that you completely bypass this function, having your pods in dev already in your workspace! Of course, if you perform the “pod installation” inside your project directory, you will simply get a mess of dependencies, meanwhile, the Pod will install according to the subfile, and your own codebases right in the same folder tree.
What I am doing is to separate the pods (which may or may not depend on other pods) separately. In addition, it’s good practice not to be in the same “workspace” of the application. And you can develop your module with a demo application.
And in the directory of the main application, I indicate "develop" the branch of my own containers in the subfile. Consequently, the application is being developed with depdencies on pods, as if these pods were published officially. Besides being simple in dev as well.
This makes you, of course, have things separate, which is not so nice when you need to change someting in the pod code for your application.
Two possibilities (none of them are very pleasant). First, change your module, and then do the "pod update" update inside your application folder.
Secondly, play with the module code directly in the application workspace (the module code was imported by the module update command). And once satisfied, the return port will change the source code of the module for fixing.
Much back and forth, but I havent found better than that.