the project panel is just a convenience panel for you to use to access your flash project's files without using a file browser. it has nothing to do with your publish settings.
if you don't see a great need to forego using your file browser, join the crowd. the project panel was an idea with no great benefit.
someone probably made a big to-do about it and got enough people to vote for the feature so adobe added the feature. and then found nobody cared so, it's not going to be in the next flash pro version.
okay. I guess ill leave it then... the only thing i needed it for was to get the flash pro and flash builder tight integration. I was hoping changing/adding library path in one IDE wud reflect a change in another but sadly it wont work that way. Ill need to manually add swc in both IDE
Thank you kglad.