Thanks. These are known bugs and there are a few others that we know of that you haven't discovered yet. I have added a warning to the installation instructions not to use the git version until the warning is removed. At this point if you are installing on a production server that you will be using with students, I would recommend using the svn version.
The git version is actually very close to WeBWorK 2.5.1 and our hope was to have a stable 2.5.1 on git before the end of the WeBWorK coding camp in Winona that just ended. However, we missed that deadline and our new deadline is about two weeks from today.
Here are a few comments about the bugs you report.
The login warning you see causes no harm at all (it is just an erroneous error message when using password authentication). There are now new versions of the the classlist editor, homework sets editor and library browser. Not all are totally developed so you have a choice of which to use and display. The current (buggy) default configuration files display none but is very easy to change. Unless you made some changes (e.g. moved the textbooks file or edited NPL-update), when you installed the library, it didn't get any textbook information to be used in advanced search. Your suggestion of using a link so that old courses don't break is exactly what I did on the new MAA server and I'll put that in the instructions. A bug you haven't discovered yet prevents solutions being displayed for problems that do have solutions.