Thanks for taking the time to do the additional tests.
I'm less familiar with the admin console part (I do know it uses some different code paths from the non-console uploading logic).
If I remember correctly the upload code for the command line case marks the uploaded file for deleteOnExit (which explains why it disappears during a controlled server shutdown). I had thought that the uploaded file itself was also deleted after the deployment had finished, but clearly that's not happening in your case.
I've also pointed some of the people who work on the admin console to this topic so they can lend their expertise. This could be a known issue but I'm not sure; they will be.
- Tim
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