Bill,
Yeah! It is OK for casual programmers especially those that don't know the difference between pde/ino and cpp
I've seen one possible solution to use #include <..\Wire\Wire.h> so if arduino team makes this change to all contributed library "import library", this may solve all the problem, will it?
pYro_65,
That'll be great! If you can intercept the commands and reassemble stuff to them, let us know!
At the moment I am developing user interfaces with LCD and keypads. I don't actually need any arduino hardware and simulated all necessary hardware (LCD, RTC, etc.) on PC 
I only occasionally need to teach arduino IDE how to compile by including libraries in the main sketch (the main sketch doesn't need all those libraries as Bill mentioned). All my work has been on Dev C++. I can say whether to look in subfolders for include files. I don't know if it is an IDE thing or there is a g++ option to look inside subfolders. Dev C++ has a horrible debugger. I can't change variable values although it says I can. Addresses are often misinterpreted so I can't see what my strings look like. Plus the variable view doesn't update itself. I'm ready to move on to a different IDE. Man. Arduino is good but maybe it's my time to move my largish project to some better IDE. Any suggestions for a good PC-based IDE that uses gcc (for my simulator) and a good arduino-compatible avr-gcc IDE?