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bits 	16 						;we start in 16 bit mode
org 	0x7C00					;and at 0x7C00

entry:							;start here!
		jmp 	load
;; print: print the string that resides in si
print:
		.printstart:
		lodsb					;move a byte from si to al
		or		al, al			;check for a zero
		jz 		.printend
		mov		ah, 0x0E
		int		10h
		jmp		.printstart

		.printend:
		ret
load:
		mov		si, stage1msg
		call 	print

		mov		ax,	0x1000		;this is where the sector is going to be read into
		mov		bx, ax
		xor		ax, ax
		mov		es, ax
		
.reset:
		mov		ah, 0x0			;function 0, reset
		mov		dl, 0x0			;drive 0
		int		0x13
		jc 		.reset			;if the carry is set, something went wrong, try again

.read:
		mov		ah, 0x02		;function 2, read
		mov		al, 1			;read 1 sector
		mov		ch, 1			;the sector past stage1, so still track 1
		mov		cl, 2			;the sector to read
		mov		dh, 0			;the head number
		mov		dl, 0			;the drive number
		int		0x13
		jc		.read

		jmp 0x1000:0x00
		
		cli
		hlt

stage1msg	db "This is stage1", 13, 10, 0		
times 510 - ($ - $$) db 0		;it needs to be 512 bytes
dw 0xAA55						;boot signature

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org 0x1000							; This sector is loaded at 0x1000:0 by the bootloader

start:
	mov 	si, msg
print:
	lodsb
	or	al, al
	jz 	out
	mov	ah, 0x0E
	int	0x13
	jmp	print
out:	
	msg 	db "This is the second stage!", 13, 10, 0
	cli								; just halt the system
	hlt

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nasm stage1.asm -f bin -o stage1
nasm stage2.asm -f bin -o stage2
cat stage1 stage2 > floppy.img
dd if=floppy.img of=/dev/sdc

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      mov      ax,   0x1000      
      mov      bx, ax                       ;<---Instead of moving 1000 to bx, move it to es and zero out bx
      xor      ax, ax
      mov      es, ax

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.read:
      mov      ah, 0x02      
      mov      al, 1         
      mov      ch, 1         ;still pretty sure track is 0
      mov      cl, 2         
      mov      dh, 0         
      mov      dl, 0         
      int      0x13
      jc      .read

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   mov   ah, 0x0E
   int   0x13                     ;pretty sure you ment int 0x10

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out:   
   msg    db "This is the second stage!", 13, 10, 0                    ;I'm not sure if this would help but I think you should move this below the rest of the code
   cli                        
   hlt                                              ;since you're only reading a sector and not using a File System you should include "times 512-($-$$) db 0" or something similar to zero out the rest of the 512 bytes

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cli                       
hlt