INPUT_FILTER being added to mainpage?

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INPUT_FILTER being added to mainpage?

I posted this on StackOverflow and have not received a response, so I am hoping someone can help here!

I am trying to use the mainpage functionality of doxygen to specify what will be displayed on the index.html page. I want my README.md file to be the index page.

I currently have set in my doxyfile:

INPUT                  = README.md /path/to/my/project/files
FILE_PATTERNS          = *.proto *.md
INPUT_FILTER           = "python /path/to/my/docs/proto2cpp.py"

Doxygen is finding the README.md and adding it to the index.html page, but it is also adding the proto2cpp.py file to the index page.  So my index page has all the code and documentation for the proto2cpp script, and then the README.md is appended at the bottom. proto2cpp is in a different directory than what is indicated in the INPUT configuration, so it must be picking it up somehow from the INPUT_FILTER?

I can't figure out how to get rid of this python script, any ideas?