Ok, I have had a quick look at upload.
I wrote TiddlerEncryptionPlugin (TEP) quite a while ago.
TEP overrides store.getSaver().externalizeTiddler and saveChanges().
saveChanges() is the code that is executed when you click the 'save
changes' button.
The Upload plugin does not override the save changes mechanism nor
does it utilise the externalizeTiddler() function.
A special version of TiddlerEncryptionPlugin would need to override
the config.macros.upload.handler.
Alternatively, it would be nice if the upload plugin actually overrode
the save code.
I am a bit busy tonight, but sometime over the next few days I may get
motivated to whip up an enhancement such that TiddlerEncryptionPlugin
will 'override' Upload plugin to allow encryption of tiddlers prior to
upload.
Unless, of course, someone beats me to it and sends me the update :-)
...Lyall