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In order to add HTML/JS/CSS content to the main site at https://finesce.github.io use the main branch on the https://github.com/FINESCE/finesce.github.io repository. This main page detailing the FINESCE project DSE list can be updated to link to the individual WP DSE’s github.io pages sites.
In order to add HTML/JS/CSS content to the github.io pages for an individual DSE, create the gh-pages orphan branch on the individual DSE repository. See the guide here: https://help.github.com/articles/creating-project-pages-manually/
An example of the github.io page for an individual DSE might look like https://finesce.github.io/wp-dse-example-gh-pages