In Vivado 2017.2, when I edit my user IP and add a file to a file group, Vivado is adding other files in the directory as well, even though I did not select them.
If an HDL file is added to a file group in the IP Packager GUI, and this file is located in the same directory as the component.xml, all of the files in the directory are added whether selected or not.
The command sent to the Packager engine use "./" instead of just the selected file.
To work around this, a user will need to either move the HDL file to another directory before adding it to the packaged IP or manually remove the extra files from the IP after adding.
This issue is fixed in Vivado 2017.3.