I just answered this question on the "public/private" sqlclr newsgroup, but now I'm wondering myself. What IS all that stuff doing in sys.assembly_files? If you've done autodeployment of a SQLCLR assembly lately, take a gander as the metadata view sys.assembly_files. There's not only the binary assembly code and the debug symbols (pdb file) but also source code. And finally, Visual Studio project file, .csproj or .vbproj.

You actually need:
  The real assembly code to run the assembly. Of course.
  The debug symbols if you want to enable in-process debugging

You might like the source code because then its stored in the database like T-SQL code is. There was a thought at one point that you'd deploy your source code and SQL Server would run a compile on it inside SQL Server. That's not gonna happen (at least this time around), and I sort of wondered why people wanted it, maybe because T-SQL stored procedures work that way, but more likely for manageability. That way the actual code is backed up with the database. Anyhow, in beta 2 the source lives in the server, but is not used by the execution engine. Interestingly, if you choose to use an external key file to codesign the assembly, maybe to deploy it to clients for deployment to their GAC, this isn't stored in the database. At least I haven't found it so far.

Still not sure why the VS project file is there though, maybe because it contains project settings you'd need if you wanted to rebuild. But you'd need the keyfile too.

BTW, if you do a "manual" deploy with CREATE ASSEMBLY only the actual binary is cataloged, of course. You can add the rest of the stuff manually with “ALTER ASSEMBLY … ADD FILE FROM …”. Or add any other file that strikes your fancy, for that matter.