Hi Christos,
That section overlap error indicates that the bootloader is too large to fit into your target device. I just tried it and got the same result - it's the MICRO board's LED driver that pushes it slightly over the edge.
The mass storage bootloader is actually closer to 6KB, with the additional 2KB of space on the smaller devices coming from an "AUX" flash section I define just before the real bootloader section on devices with the smaller bootloader area. Functions in the bootloader code are then relocated into that AUX section (except for the flash functions, which are required to be in the bootloader section to work correctly) via the AUX_BOOT_SECTION macro used in the bootloader source code.
Unfortunately, that macro can't easily be applied to the inner library functions, so a bunch of flash in the bootloader space is taken up by (for example) the ISR handlers and USB control processing code. If there's enough interest I can add in a new compile time token to optionally move those over, but picking which functions to move could be a chore for the end-user. I've taken another look through the MAP file and can't see any easy targets I've missed, so the one quick fix I can suggest for now would be to use BOARD=NONE in your makefile to just disable the board LED drivers. It'll still work fine, but without the visual indicators.
- Dean
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I've just tried that configuration, and it compiles successfully for me on the latest LUFA HEAD (2cde257fe), using the latest Atmel Toolchain (avr-gcc (AVR_8_bit_GNU_Toolchain_3.6.0_1734) 5.4.0).
You are using WinAVR which is positively *ancient* at this point - heck, I started with that nearly a decade ago, and it hasn't been updated for many, many years. I'd strongly suggest ditching it and switching to the latest toolchain instead for the bug fixes and better optimization support - there's a standalone version at http://www.atmel.com/tools/atmelavrtoolchainforwindows.aspx if you don't want all of Atmel Studio.
Cheers!
- Dean