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Code-Glosser, currently, can only markup a directory. This is because the file used to preserve the current session, session.json keeps track of the state of all files relative to the directory it is stored in. Being able to do it for individual files would be unfeasible, and unnecessary because you the exported files are only those that you markup.
When you launch the application, you will see a window like such:
You MUST select a directory: That is not a file, but a directory. Like such:
After this, select any given file from the directories. Note that this application is in Alpha, selecting a file that cannot normally be opened will cause it to crash (for now). See that I select src/kernel/mem.c
Double click on it and it should bring up the code, syntax highlighted
If you need more information, see the Code-Glosser demo on the README.md, as it will demonstrate how to begin marking up.