I just tried doctree for the first time on a Python project.
It's a serverless.com deployed project and I noticed that when I run doctree index ., files in my node_modules directory were indexed as well - this included all the markdown files in the node_modules and some go files that are part of the serverless npm package (some templates from what it looks like).

I didn't find any similar issues yet but I think it generally might be a good idea to not index files in .gitignore, or provide a different mechanism to allow me to ignore certain files or directories.