Copying Doxygen Documentation from gh-pages branch into a subfolder of Master branch

Solution 1:

You can go on as is (upload the documentation in the gh-branch), but add one more step:

 git submodule update --remote

You can declare a branch content as submodule of another branch

git checkout master
git rm -r gh-pages # save your data first
git submodule add -b gh-pages -- /remote/url/of/your/own/repo
git commit -m "ADd gh-pages branch as submodule"
git push

Since that submodule will follow the latest commit of its own branch, a git submodule update --remote done in master will be enough to update the content of the gh-pages subfolder (root directory of the submodule).

Note: Since August 2016, you can publish your pages right from the master branch (not always the gh-pages branch)

That would simplify your issue.