Add note about debugging settings.

They appear to be part of the per-user state.
Pad script numbers with leading 0 in the scripts dialog.
Don't wait for exit twice.

Perhaps this was the cause of the irregular hangs?
Update version numbers and add new installer.

The AssemblyVersion is what the vsixver.py script fishes out, but the
source.extension.vsixmanifest version is what's displayed in the
Extensions and Updates dialog, and what the VSIX installer uses to
figure out whether the package is actually an update or not (and, if it
isn't, refuse to install it).

*weary face*... should really fix that.