Sorry, I have no idea. Never really thought about it to be honest lol. Just looked around the files but I can't find anywhere where the flags would be stored. Same on 2.3, looked through all files / database can't find anything so I don't think it's possible to see where they are created/stored on 2.3, dunno about Ruby. Like I said I don't know much about Ruby files as I've never used them, so maybe IceMan or someone else who's had experience with the files could reply to help you, or give him a PM.
Edit:
You could always combine namelists with flags I suppose, for example:
[@OnLogin]
#IF
CHECK [150] 1
#ACT
break
#ELSEACT
SENDALLMSG "<$USERNAME> joined the server. Welcome!"
SET [150] 1
addnamelist ..\Npc_Def\FlagLists\150.txt
so it sets your flag [150] on and also adds your name to the namelist in npc_def\flaglists folder so you can see if you have the flag on or not, but it would mean creating a lot of text files if you use flags alot lol. Other than that I dunno sorry.