Adds a section at the very end to document all flags and links
to it from every function that takes a flag argument.

Fixes: nodejs#16971

Removed description of flags into one place, linking to it from all
other references.

Also rearranged the flags alphabetically, keeping connected ones
together.

Fixes: nodejs#16971

Removed unnecessary newlines from the end of document

Finally able to resolve the merge conflicts

All changes in the previous commits, consolidated location,
adding periods, putting notes together were wiped away by my
clumsy merge. Redid them all!

Two trailing tabs caught by the linter
removed