Chipping in my 2 cents here...
On the "policy"/legal question of whether it's permissible to package the internal open source in this larger source for the Debian project, I have no specific opinion but it sounds complicated. You might
I do. Remember the GPL's mantra: "Free as in speech". The software should be available for anyone, without any obstacles in obtaining it. To me, it is clearly a violation of its own license.
Granted, you might be able to download the part, safely cut it out of whatever proprietary software is around it, but the next distribution (Redhat, Arch, FreeBSD) might run into the same issue.
Thus, finding a way to make the AmberTools downloadable without the need to register is the better solution. Either by asking NICELY, or by making it available on a different website.
gauge upstream's feelings by asking if they can provide a tarball with just the open source parts. If not, even if your interpretation of the license situation is that you can package the inner code, it may not be worth it if it's fought by upstream. (E.g. they may see their more restrictive license as "additional terms" on top of the license in the inner files, thus basically creating a non-open source license.) Of course I am not a lawyer, just noting that it's much more pleasant to package when upstream is cooperative or at least not hostile :)\
Having to register to download software is not free software. It is open source. That is a difference.
(Also not a lawyer. ;) ) Thomas
