1. How do they all work ?

Simple.  There's /waffle/extern/_system for the normal
commands, and you can add any command you want with any access
you want by adding a corresponding file to the /waffle/extern
directory.  The file that you create corresponds to the name of
the new command.  Be very careful regarding security, though,
as externs can be the least secure part of Waffle.

2. I use 4DOS, yet Waffle shells out to DOS, not 4DOS...

You need to change the command interpreter in /waffle/extern/_system
to use 4DOS rather than command.com

3. If I implement Waffle as a door from another BBS, how can users exit
    from Waffle without dropping carrier?

First, disable the `exit' command in Waffle by adding the
following line to your static file.

        disable: exit

Then provide an external implementation of the exit command by
creating extern/exit with the following contents.

        /access=0 /logout=exit /log /exit=81

This causes Waffle to exit, without dropping the modem connection,
with errorlevel 81 (or whatever level you want to specify).  The
/access=0 ensures that all Waffle users can get back out once they
get in.  Then you just trap errorlevel 81 in the batch file that
started Waffle to go back to the other BBS.