I have SDFat installed. I didn't try to compile the sd card hex uploader, but Atmega_Board_Programmer and here are the error messages:
In file included from Atmega_Board_Programmer.cpp:121:0:
bootloader_atmega168.h:3:34: error: variable ‘atmega168_optiboot’ must be const in order to be put into read-only section by means of ‘__attribute__((progmem))’
In file included from Atmega_Board_Programmer.cpp:122:0:
bootloader_atmega328.h:3:34: error: variable ‘atmega328_optiboot’ must be const in order to be put into read-only section by means of ‘__attribute__((progmem))’
In file included from Atmega_Board_Programmer.cpp:123:0:
bootloader_atmega2560_v2.h:3:29: error: variable ‘atmega2560_v2’ must be const in order to be put into read-only section by means of ‘__attribute__((progmem))’
In file included from Atmega_Board_Programmer.cpp:124:0:
bootloader_atmega1284.h:5:40: error: variable ‘optiboot_atmega1284p_hex’ must be const in order to be put into read-only section by means of ‘__attribute__((progmem))’
In file included from Atmega_Board_Programmer.cpp:125:0:
bootloader_lilypad328.h:5:53: error: variable ‘ATmegaBOOT_168_atmega328_pro_8MHz_hex’ must be const in order to be put into read-only section by means of ‘__attribute__((progmem))’
In file included from Atmega_Board_Programmer.cpp:126:0:
bootloader_atmega1280.h:5:45: error: variable ‘ATmegaBOOT_168_atmega1280_hex’ must be const in order to be put into read-only section by means of ‘__attribute__((progmem))’
Atmega_Board_Programmer.cpp:223:3: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
Atmega_Board_Programmer.cpp:223:3: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
Atmega_Board_Programmer.cpp:223:3: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
Atmega_Board_Programmer.cpp:223:3: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
Atmega_Board_Programmer.cpp:223:3: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
Atmega_Board_Programmer.cpp:223:3: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
Atmega_Board_Programmer.cpp:223:3: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
Atmega_Board_Programmer.cpp:223:3: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
Atmega_Board_Programmer.cpp:223:3: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
Atmega_Board_Programmer.cpp:223:3: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
Atmega_Board_Programmer.cpp:223:3: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
Atmega_Board_Programmer.cpp:223:3: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
Atmega_Board_Programmer.cpp:223:3: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
Atmega_Board_Programmer.cpp:223:3: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
Atmega_Board_Programmer.cpp:223:3: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
Atmega_Board_Programmer.cpp:223:3: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
Atmega_Board_Programmer.cpp:223:3: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
Atmega_Board_Programmer.cpp:223:3: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
Atmega_Board_Programmer.cpp:223:3: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
Atmega_Board_Programmer.cpp:223:3: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
Atmega_Board_Programmer.cpp:223:3: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
Atmega_Board_Programmer.cpp:223:3: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
Atmega_Board_Programmer.cpp:223:3: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
Atmega_Board_Programmer.cpp:223:3: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
Atmega_Board_Programmer.cpp:223:3: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
Atmega_Board_Programmer.cpp:223:3: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
Atmega_Board_Programmer.cpp: In function ‘byte writeFlash(long unsigned int, byte)’:
Atmega_Board_Programmer.cpp:262:3: warning: no return statement in function returning non-void [-Wreturn-type]
Atmega_Board_Programmer.cpp: In function ‘void showHex(byte, boolean, boolean)’:
Atmega_Board_Programmer.cpp:270:71: warning: narrowing conversion of ‘((((int)(b >> 4)) & 255) | 48)’ from ‘int’ to ‘char’ inside { } is ill-formed in C++11 [-Wnarrowing]
Atmega_Board_Programmer.cpp:270:71: warning: narrowing conversion of ‘((((int)b) & 15) | 48)’ from ‘int’ to ‘char’ inside { } is ill-formed in C++11 [-Wnarrowing]
Atmega_Board_Programmer.cpp: In function ‘void writeBootloader()’:
Atmega_Board_Programmer.cpp:415:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Atmega_Board_Programmer.cpp:438:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Atmega_Board_Programmer.cpp:354:8: warning: unused variable ‘lFuse’ [-Wunused-variable]
Atmega_Board_Programmer.cpp: In function ‘void getSignature()’:
Atmega_Board_Programmer.cpp:526:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]