@BobHanson The SwingJS-site.zip file is in ./swingjs as you'll expect. 
It gets unzipped to a transfer location (and not to the actual site location 
to avoid the unzip happening again unecessarily when something changes in that location, 
e.g. an Eclipse IDE on-the-fly transpile) which is ./build/jalviewjs/tmp/site_swingjs/.

In the meantime, if you're using Eclipse as IDE, it should be transpiling directly 
into the actual site location, which is ./build/jalviewjs/site, and if you run the task 
jalviewjsIDE_PrepareSite (under the Gradle Tasks tab) it will sync the files 
from ./build/jalviewjs/tmp/site_swingjs/ to ./build/jalviewjs/site/ (along with other unzipped 
files such as those in ./utils/jalviewjs/libjs/*.zip and files from ./utils/jalviewjs/site-resources/).

If you run the task jalviewjsIDE_AssembleSite it will (/should) also build cores 
into ./build/jalviewjs/tmp/site_core/ and then sync them to ./build/jalviewjs/site/.

The _j2sclasslist.txt that gets used to build core_jalview.js is ./utils/jalviewjs/_j2sclasslist.txt, 
whereas other lists are that are used to build cores are all the files found in ./utils/jalviewjs/classlists/.
Basically all the stuff that gradle uses to build jalviewjs is found in ./utils/jalviewjs with 
the exception of ./swingjs, which I know you wanted as-is in the top-level.