Opening up the gearbox

If you remove the clutch actuating arm you will see the nut on the end of the main shaft. This nut needs to be undone before the inner cover can be removed.

Covered in the gearbox section of the manual, as attached:
 

All of the gearbox studs and nuts have right-hands threads except for the rear chain sprocket nut/shaft. This is better known as the Sleeve Gear. The gearbox Mainshaft passes through the Sleeve Gear and has right-hand threads at both ends.
As follows is very handy Trouble Shooting Guide........
 

GEARBOX TROUBLE SHOOTING GUIDE

Symptom                                                   Cause

Kickstart lever does not engage.      -       Worn kickstart pawl

Kickstart engaging under load.         -       Worn lay-shaft bearing in Shell or Broken Lay-shaft 

Cannot engage 1st &/or 4th gear     -       Incorrect meshing of quadrant with the cam-plate 

Engaging false neutrals                    -       Incorrect meshing of quadrant with the cam-plate

Difficulty shifting between all gears   -      Bent mainshaft  or bent layshaft

Difficulty selecting gears        -      Selector spring upside down or broken (weak)

Gearbox will shift up but not down    -      Return spring broken 

Gear lever will not return to mid position     -      Broken return spring

Jumps out of 1st gear under load       -     Worn engagement holes in lay-shaft 1st gear

Loss of 1st &/or 2nd gear.                  -      Broken lay-shaft

Grinding noise in 1st gear under load    -    Broken lay-shaft

Loss of 3rd &/or 4th gears                  -     Worn mainshaft bearing in inner cover

Whine in lower gears                          -       Worn bush in kickstart axle

Cannot engage neutral when bike is stopped   -   Clutch needs cleaning &/or adjustment;

                                                                          -   or incorrectly adjusted primary chain;

Loss of clearance between sprocket and shell  -  Sleeve gear bearing loose in gearbox shell

Grinding &/or chattering noise under load  -  Broken gear tooth / teeth

Sloppy gear selection       -     Too much mainshaft &/or lay-shaft end-float

                                          -     or worn thrust washer (Lay-down only)

Greater experts than I have posted here...but surely the original question was: must the clutch be removed before removing the gearbox inner cover?  Surely not?
(Edit...sorry Ian...you did answer...I ought to go back to sleep...)