"apt-get install boinc" puts new boinc versions in some different place from where the .sh, run from my Downloads directory, places them. Should I copy the .sh file to some other directory to make it work?

I've never tried to copy over the Berkeley binaries to where the package maintainers put them. If you're not feeling the need to upgrade to each alpha build, I'd let apt-get and the package maintainers deal with it.

If you're interested in some of the features you can get with the apt-get install and *aren't* afraid of the command line, I can point you toward install instructions that use the Berkeley binaries.

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Kathryn :o)