I was able to take the folders of symfony project and placed them on dropbox with git. Merged the latest sf2 standard distro with the tree of my project then manually added submodules to my project. I could not find a way that the .gitmodules could revert back how it was initially generated. But at any rate I was able to do it and learn on my way the names and perhaps speculate about what each component do for sf2.
My experience from one day invested on this is, do not do it, yes you hear well, do not even try.
Use symfony2project or the distro and then adapt it little by little, but never try to merge files.
If the default complete system is not in place it is a waste of time to try to rebuild sf2.