When working with a worpress site with lots of custom post types and lots of page templates, my theme folder is looking messy. What are the accepted best practices to organise code files in WordPress?
a couple of the limitations i'm coming up against are that templates are chosen by name, so i can't group files by prefixing them. Also custom post template files can not be in sub directories. Also header and footer can not be in subdirectories.
How can i organise my code better?