Subtree merge

You can merge repository A into a subdirectory of a project B using the subtree merge strategy. This is described in Subtree Merging and You by Markus Prinz.

git remote add -f Bproject /path/to/B
git merge -s ours --no-commit Bproject/master
git read-tree --prefix=dir-B/ -u Bproject/master
git commit -m "Merge B project as our subdirectory"
git pull -s subtree Bproject master

If you want to merge project-a into project-b:

cd path/to/project-b
git remote add project-a path/to/project-a
git fetch project-a
git merge project-a/master # or whichever branch you want to merge