The "add to tools" checkbox which adds a tool to the scientists Tools menu only shows on the script tab when a script is run, not on the "params" tab. It should appear regardless of which tab is showing.
I made the change for this a couple of weeks ago (2021 July 13 to JythonUtil.java, r23869) and I didn't notice this breaks one of the paths where this GUI is used:
This is fixed. Also I'd like to add the following tool tip to explain the script security:
"""Autoplot keeps track of what scripts you have run, and when
things change with a script you will be asked to verify
the script. Scripts can be made which delete files, so be
sure to only run scripts from people you trust."""
Last edit: Jeremy Faden 2021-08-01
Also, there's a differences engine within Autoplot's source now, and it should be used to annotate parts of the script which change.