The easiest way to support DotChart is to purchase the In-App purchase within the app itself. It will remove some limitations. If you like using DotChart, take a minute and leave a review on the App Store. That helps a ton!
DotChart is distributed on the Mac App Store and is a sandboxed application with restricted access to the files. For the command line tool to be able to access files, you need to explicitly select a folder.
If you create the symlink for convenience, you just need to run the command dotchart in a Terminal window. The DotChart command takes a Markdown file as input and generates an PNG file as output.