In a quick new post to his site Michael Kimsal asks an interesting question that some PHP developers don't think about in the course of their development: "Is your code portable to subfolders?.
Have been dealing with a couple of PHP projects recently which have been a far bigger pain in the backside than I anticipated, and both had some of the same stumbling blocks. In both cases, and in other projects I've seen, there's a huge assumption that the code will be run from the root of a domain, and all url and routing management have this assumption baked in to everything they touch. What's the answer?
Some projects just suggest making a new virtual host in the web server configuration and moving on, but this isn't always a real possibility for some projects. In some recent experience, he's found several of the major PHP frameworks assume this kind of setup. He mentions a Java framework, Spring, that allows for this kind of redirect and wonders why it's not that easy in something like Slim.
Maybe try grabbing your own code sometime and reinstalling it in a 'non-traditional' way, and see how many assumptions you've baked in are really necessary, vs just using defaults.