I appreciate you continuing to look at my question John.
By "base" do you mean the web root being served by apache?
If you take a closer look at the the system paths I listed, there are two "public"s in the mix. The higher one is in the user's home directory and it the target of mod_userdir rewriting - it is effectively the web root. The lower "public" is CI's exposed assets directory. Since the URL is resolving and CI is bootstrapping just fine, I am still pretty sure this is not a framework path issue, since then wouldn't the whole thing not run?
Where does the router class get the base from which to separate the controller and method segments of the url?
Why is setting baseUrl (/app/Config/App.php) and RewriteBase (public/.htaccess) not doing the trick?
Earlier today I went ahead and changed all the mod_userdir targets to be "~/www" instead of "~/public" is case the two publics were choking mod_rewrite. The CI router still isn't resolving controllers properly so that wasn't it.
Considering your suggestion further, if I looked at how to place app/ sys/ writeable/ etc. above ~/www/ (directly in the user's home directory) encapsulating the instance into a git repo would get messy. Part of the reason I'm trying to have students be able to simply composer-install the starter app into a subdirectory of their personalized web root is so that they can use git to collaborate and submit work to me.
