Autoplot is software which is supported through a NASA grant, and by people using it for their research. It runs on the Java platform, and will only make modifications to a folder in your home directory, adding a directory called "autoplot_data". When used to look at data on remote websites, it will load the data into directories within this area. Autoplot can also run scripts, and when scripts are run, they could be written to write outside this area, so do not run scripts if you do not trust with the script author. Thanks for asking the question!
Jeremy