I appreciate your answering, because this does sound goofy.
The original, Evo-based site is on a public-facing Web host. I brought it down to my own, non-Web-exposed machine to work on it. Once I've completed the Revo port, back up it goes to the Web host. And with it go any artifacts (i.e., obsolete file junk and potential genuine infestations) that came along with it.
I don't know if the reported files are the original files that came in both the Evo and Revo versions of TinyMCE.
Once I'm done with the Revo port, I think I should walk through the site and delete the obsolete stuff, file by file.
I join you in supposing that this new CLAM revision has made false detections. If so, anyone else updating to Ubuntu 12.04 and running CLAM will see the same complaints. Neither false positives nor genuine problems are helpful to the MODx reputation, so I thought I ought to report them.
The CLAM team provides a way to report false positives (at
http://www.clamav.net/lang/en/sendvirus/), but I don't think ordinary MODx civilians like me ought to be claiming true or false virus problems on behalf of MODx. That would make for chaos.