The startup process looks like this right now:

• gnucash is a hybrid /bin/sh and guile script which first execs gnucash-env on itself to set up the proper environment and then run the rest of the code in the gnucash file as a guile script.
• from the gnucash script itself, the (gnucash bootstrap) is loaded, and then control transfers to the scheme function, main.
• the current module is set to (gnucash bootstrap) -- this is a hack and should change later.
• gnc:main is called to finish starting up the application.
• parse the command line
• load the system config if we haven't already (there's a command-line option to load the file earlier, --load-system-config)
• load the user's ~/gnucash/config.user if it exists, otherwise load the user's ~/gnucash/config.auto if it exists.

config.auto is where we'll eventually spit out UI selected prefs.