The nightly builds are a little way behind the development branches at the moment so not all the code has been merged across yet, however as you might expected "My Files" will link you to the current users "User Home" and "Shared Files" will go to a new location within "Company Home" that can be used for simple collaboration outside of sites.
The nightly builds are against trunk, however development now takes place on separate branches before being merged to head. We have been re-working our processes in the past year so there have not been as many commits directly to trunk, however when merges are made to trunk in the future they are likely to contain large numbers of changes.