I need to make sure a custom build tool that operates on a lot of files is always run when one of those files are changed.
I know you can specify "Additional Dependencies" for the custom build tool, but is there a better way than specifying one file per line?
"Additional Dependencies" is the correct and only documented way. You could adjust the contents of this field for the build tool in the Project file using an external tool to save on the troubles of doing a copy & paste & typo-adjust.