Actually, creating a workspace doesn't solve the issue.  The problem is that the implicit dependency resolution only works when building a scheme (from what I can tell).  A scheme isn't created until the project / workspace is opened.

I think what I suggested works well though.  Add target references for all of a Pods dependencies to the Target Dependencies phase.  This alone resolves the command line building.  To address #731, just remove the library references from the Frameworks Build Phase and add the linker flags to a private xcconfig file for the integration library (libPods.a).

This does generate an aggregate static library, but through linking, not through lipo.  So the result is a single libPods.a (and libPods-target-definition.a for other target definitions).  

If an end user needs the whole project to build from the command line without generating a scheme, then there is still a problem, but this doesn't work today either, and it can't be solved with a target dependency because you can't add target dependencies across projects in a workspace.  Although, you can add a target dependency from another project that is in a parent projects embedded workspace... but I think I've gotten off topic here.