I would like to recomend you to read about Modules and DDD (Domain-Driven-Design). After you understand the theory behind those architectures, you can use it, adapting for the needs of your project.
I faced that same issue, just a month ago. I started to have too many files, and the default organization of folders became a hell for me. I decided to follow the DDD architecture, but sometimes DDD can be massive, mainly for small to medium applications. So i adapted it, to be more simple, at least for now...
I considered creating my architecture based on Modules too, but I thought it will not fit perfectly for the project.
I'm also using the Repositories Pattern, together with DDD, yes! It's completely possible to mix all patterns you REALLY NEED! (make sure you really need it before implementing, cause those patterns come with complexity for your software).
There is a lot of software architecture and archtypes patterns (and philosophies), you can use MVC together with DDD or SOA (Services Oriented Architecture), and Repositories with Active Record (the Eloquent), and etc etc etc.