OldFatGuy: did GoG forget to scan the whole manual into the PDF file? 
  No, the look of the manual is a deliberate design choice by Zachtronics. It’s supposed to look like a scanned paper document, reminiscent of the old paper manuals from the 1980’s/1990’s. The look is part of the visual storytelling that fits the narrative in the game.  
 It immediately gave me flashbacks to the good old C=64 programming handbook ;)  
 And the manual is indeed complete.  
 You only have the registers:  
ACC, BAK, NIL   The ports:  
LEFT, RIGHT, UP, DOWN, ANY, LAST   Comment, label, breakpoint:  
#, :, !   Arithmetic instructions:  
ADD, SUB, NEG, NOP   Register and port related instructions  
MOV, SWP, SAV   Jump instructions:  
JMP, JEZ, JNZ, JGZ, JLZ, JRO   And the visualization module command sequences   
 Being a code golfer and a fan of esoteric programming languages, I can see that they are even being generous with the instruction set. I mean, who needs SUB if you have ADD and NEG, for example? ;)