Git Merge - Incomplete, Missing files and Folders

Question

I was trying to merge a dev branch into master.

git checkout master    
git pull . dev

Everything seemed to go well, although there were co

Answer 1

It sounds like git thinks that the missing files were deleted on the master at some point between where it branches from dev and the pre-merge head. That's the only reason I can think of for why git would silently drop tracked files during a merge.

Unfortunately, I don't know a good way to fix that. I'd probably just re-add all the deleted files from the dev branch manually (or with a little bit of bash scripting), and then to a git commit --amend to revise the merge commit to include them.