LTO and naked functions?

I am having trouble getting a FreeRTOS project to build with -flto. It builds fine without the -flto flag.

It's complaining about symbols used in __attribute__(( naked)), (assembly-only) functions. Any ideas what may be going on?

ARCH_FLAGS = -mthumb -mcpu=cortex-m0plus
CFLAGS = $(ARCH_FLAGS) -std=c99 -g3 -ffunction-sections -fdata-sections -Wall -flto -fpic -Os
LFLAGS = $(ARCH_FLAGS) -Wl,--gc-sections -Wl,-Map=$(NAME).map --specs=nosys.specs -T$(LD_SCRIPT)

$(NAME).elf: $(SRCS)
 $(CC) $^ $(CFLAGS) $(LFLAGS) -o $@ -lm
 arm-none-eabi-size $@

`pxCurrentTCB' referenced in section `.text.vPortStartFirstTask' of C:\Users\amastro\AppData\Local\Temp\ccVReNMj.ltrans0.ltrans.o: defined in discarded section `.text' of C:\Users\amastro\AppData\Local\Temp\ccp3jDRf.o (symbol from plugin)
`vTaskSwitchContext' referenced in section `.text.PendSV_Handler' of C:\Users\amastro\AppData\Local\Temp\ccVReNMj.ltrans0.ltrans.o: defined in discarded section `.text' of C:\Users\amastro\AppData\Local\Temp\ccp3jDRf.o (symbol from plugin)
`pxCurrentTCB' referenced in section `.text.PendSV_Handler' of C:\Users\amastro\AppData\Local\Temp\ccVReNMj.ltrans0.ltrans.o: defined in discarded section `.text' of C:\Users\amastro\AppData\Local\Temp\ccp3jDRf.o (symbol from plugin)

Here are the declarations and definitions for PendSV_Handler

platforms\atsamr21g18\FreeRTOSConfig.h:72:9:#define xPortPendSVHandler PendSV_Handler
platforms\atsamr21g18\freertos\port.c:111:6:void xPortPendSVHandler( void ) __attribute__ (( naked ));

void xPortPendSVHandler( void )
{
 /* This is a naked function. */

 __asm volatile
 (
 " mrs r0, psp \n"
 " \n"
 " ldr r3, pxCurrentTCBConst \n" /* Get the location of the current TCB. */
 " ldr r2, [r3] \n"
 " \n"
 " sub r0, r0, #32 \n" /* Make space for the remaining low registers. */
 " str r0, [r2] \n" /* Save the new top of stack. */
 " stmia r0!, {r4-r7} \n" /* Store the low registers that are not saved automatically. */
 " mov r4, r8 \n" /* Store the high registers. */
 " mov r5, r9 \n"
 " mov r6, r10 \n"
 " mov r7, r11 \n"
 " stmia r0!, {r4-r7} \n"
 " \n"
 " push {r3, r14} \n"
 " cpsid i \n"
 " bl vTaskSwitchContext \n"
 " cpsie i \n"
 " pop {r2, r3} \n" /* lr goes in r3. r2 now holds tcb pointer. */
 " \n"
 " ldr r1, [r2] \n"
 " ldr r0, [r1] \n" /* The first item in pxCurrentTCB is the task top of stack. */
 " add r0, r0, #16 \n" /* Move to the high registers. */
 " ldmia r0!, {r4-r7} \n" /* Pop the high registers. */
 " mov r8, r4 \n"
 " mov r9, r5 \n"
 " mov r10, r6 \n"
 " mov r11, r7 \n"
 " \n"
 " msr psp, r0 \n" /* Remember the new top of stack for the task. */
 " \n"
 " sub r0, r0, #32 \n" /* Go back for the low registers that are not automatically restored. */
 " ldmia r0!, {r4-r7} \n" /* Pop low registers. */
 " \n"
 " bx r3 \n"
 " \n"
 " .align 2 \n"
 "pxCurrentTCBConst: .word pxCurrentTCB "
 );
}

platforms\atsamr21g18\freertos\port.c:118:13:static void vPortStartFirstTask( void ) __attribute__ (( naked ));

void vPortStartFirstTask( void )
{
 /* The MSP stack is not reset as, unlike on M3/4 parts, there is no vector
 table offset register that can be used to locate the initial stack value.
 Not all M0 parts have the application vector table at address 0. */
 __asm volatile(
 " ldr r2, pxCurrentTCBConst2 \n" /* Obtain location of pxCurrentTCB. */
 " ldr r3, [r2] \n"
 " ldr r0, [r3] \n" /* The first item in pxCurrentTCB is the task top of stack. */
 " add r0, #32 \n" /* Discard everything up to r0. */
 " msr psp, r0 \n" /* This is now the new top of stack to use in the task. */
 " movs r0, #2 \n" /* Switch to the psp stack. */
 " msr CONTROL, r0 \n"
 " pop {r0-r5} \n" /* Pop the registers that are saved automatically. */
 " mov lr, r5 \n" /* lr is now in r5. */
 " cpsie i \n" /* The first task has its context and interrupts can be enabled. */
 " pop {pc} \n" /* Finally, pop the PC to jump to the user defined task code. */
 " \n"
 " .align 2 \n"
 "pxCurrentTCBConst2: .word pxCurrentTCB "
      );
}