Hi Gustaf,
I don't worry much about the application packages, because we don't use much of them, and do not customize them.
We also have very few "embedded" JavaScript. We do have all those Sencha widgets, but I understand these are not affected.
We've got one special problem with a number of *.js.adp files. This is to use the OpenACS localization infrastructure for JavaScript files. Also we sometimes "embedd" small pieces of data from the database in a Sencha "store" (=table) in JSON code generated in the .tcl part of such pages.
The problem is that we need to make OpenACS to produce a JavaScript MIME type for these files, instead of text/html...
Cheers
Frank