It would be good to be able to include more stuff in the sketch folder. The idea is to be able to give the sketch folder to other people as-is, and they can compile the sketch without having to hunt down some libraries, etc.
eg. Libraries - they could go in a folder called 'libraries' inside the sketch folder. I could put the library dependencies for my sketch inside there. The IDE could look in there first when trying to compile the sketch.
Another problem is the HID file for Leonardos. There's currently no way for me to provide a custom HID for my sketch. It would be good if I could put HID.cpp, USBAPI.h, etc. somwhere inside my sketch folder (maybe inside a special folder called 'HID').
In fact .... it might be good to be able to put a folder called 'core' inside my sketch folder and the IDE would compile the core files from there instead of looking in "...\hardware\arduino\cores" (or wherever).
Having a 'core' folder inside my sketch folder solves the HID problem and many others, eg. If I want to reclaim Timer0 or if my sketch requires a particular Tiny85 core. With a 'core' folder I can just set up my custome core as needed and other people could use my sketch easily without any installation problems or messing up their Arduino installation. Just copy my sketch in to their 'projects' folder, job done.