The best replacement for subdirectories is subdomains.

The best alternatives to subdirectories are rated as following:
★★★★★  subdomains

Your alternative for subdirectories is not listed? Suggest!
Speaking about subdirectories, one probably shouldn't forget about makefile.

Other search terms related to subdirectories and their ratings are:
★★★★★ makefile
★★★★ automake
You have in mind a companion for subdirectories and it is not yet here? Propose!



Google Trends

Scale is based on the average worldwide traffic of subdirectories in all years. Click on graph for more.
subdirectories
subdomains