How does firmware upgrage work?
I have setup a pfSense 1.0RC box at home to work also as a PDC (Samba3) and MLDonkey p2p downloads daemon for the home computers (just 3). I know it's not very wise to do so but I care much more about features than about security at my home setup.
My understanding is that if I perform a firmware upgrade to pfSense it'll just modify the original program files and will leave untouched the Samba and MLDonkey config and program files. However I would like to know for sure if that is the case.
As the additional applications are not part of the upgrade they won't be overwritten or touched. However if you changed some startupfile to run the apps automatically on boot other than using hidden config.xml mojo you might need to touch them again after upgrade. On the other hand you are performing an upgrade of a really old version to something recent. In case things break you should be prepared to reinstall from scratch.