Possible init manifest bug

[tro3]

An unexpected behavior found during adding integration tests. Test cases mentioned are in #265, which will make this hard to follow. I just want to log it here so it is not buried in the #265 discussion.

In the test cases init/case2 and init/case3, there are two code files, the first of which references the second and one of two fixed remote repos. That repo and the second code file each reference the second remote repo. In case2, only the second repo is previously imported, and init results in a manifest with only the second repo present. In case3, only the first repo is previously imported, yet both repos show up in the manifest. One or the other seems incorrect.

[tro3]

Holding for upgraded init definition