Here is how set.mm should be patched.  I tried it and it worked.

Now the only problem is commenting it so it's not totally confusing to
someone trying to learn logic independent of set theory...

Norm

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Step 1:  Delete "$c class $."

Steps 2a through 2d:  Delete statements cv, wceq, wcel, and wsbc.

Going back to top of file, continue down:

Step 3: Replace "weq $a wff x = y $." with this:

   $c class $.
   ${
     $v A $.
     $v B $.
     wceq.cA $f class A $.
     wceq.cB $f class B $.
     cv $a class x $.
     wceq $a wff A = B $.
   $}
   weq $p wff x = y $= vx cv vy cv wceq $.


Step 4:  Replace "wel $a wff x e. y $." with this:

   ${
     $v A $.
     $v B $.
     wcel.cA $f class A $.
     wcel.cB $f class B $.
     wcel $a wff A e. B $.
   $}
   wel $p wff x e. y $= vx cv vy cv wcel $.


Step 5:  Replace "wsb $a wff [ y / x ] ph $." with this:

   ${
     $v A $.
     wsbc.cA $f class A $.
     wsbc $a wff [ A / x ] ph $.
   $}
   wsb $p wff [ y / x ] ph $= wph vx vy cv wsbc $.