The sf.net demo site is a case in point where we're stuck with having "cgi-bin/" padding out every URL including entry points. The user also has to land on ".../main.cgi" which is a bit clumsy, albeit soluble (by adding a dispatcher plugin). One quick & simple solution is to have a static landing page "/app1/index.html" with the app's look & feel, that has link(s) to the app. On sf.net this would also need a file .htaccess containing "Options Indexes".
An alternative, but slightly less simple, solution is to implement a redirect from "/app1/index.html".
Users who require query params in their landing point [see enhancement for Organization] would either stay with the current landing point or have their own static landing page.
The "Organizations" enhancement is ticket:
https://sourceforge.net/tracker2/?func=detail&aid=2356979&group_id=244452&atid=1125742