Understandable to make something different to the Arduino IDE for real experts but why not make expert mode an option and default to compatibility with all the existing Arduino open source projects?
By not supporting multiple .ino files in the normal way this becomes less of an Arduino plugin and more of an AVR plugin? Useful but quite different to how Arduino works.
There are some really brilliant and huge Arduino projects out there. ArduPilot, MultiWii being two. Both rely heavily on modular pde/ino files and libraries and will not compile with your IDE. If this is a decision that both of you have made for Eclipse and Linux then I respect that but it will reduce usability for the community.
As concerns someone reporting your IDE not to work. IGNORE that statement, it's early days for your project and every plugin has it's problems at times. Less so as more users work with it.
Best of luck