First to avoid conflicts, move all files (including dotfiles) into a subfolder and commit.
Then merge the 2 repositories with the example script below (from: https://stackoverflow.com/a/10548919/856151).
cd path/to/project-b
git remote add project-a path/to/project-a
git fetch project-a --tags
git merge --allow-unrelated-histories project-a/master # or whichever branch you want to merge
git remote remove project-a
--allow-unrelated-histories
is the "keyword" since Git 2.9.
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