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Namespaced proto and protocol apps (#268)
The protocol and proto apps were not being namespaced because I missed appending a trailing '.' to the root module names, this meant both were being excluded. Circling back, I don't know why I was excluding any of the deps apps from namespacing, as it seems to work fine with it. It was also possisble to apply namespacing to modules that were already namespaced, so I added a check to ensure that doesn't happen. This was happening for plugins in external projects, as the plugin is a dep, but the code is written to the .lexical directory.
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