Git setup for new repo

Assuming TGT_DIR will be the repository dir

cd $TGT_DIR
git init
git add {files to add}
git commit -m "First Commit"
git remote add origin {https://github.com/.....}
git config credential.helper store
git fetch
git merge origin/master --allow-unrelated-histories
git push origin master

Merging with upstream repo

cd $TGT_DIR
git remote add upstream https://github.com/--fork repo --
git remote -v
git fetch upstream
git merge upstream/master
See this

if anything went wrong try this .... git reset