How to stage a tree with all changes?

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Suppose I have a number of changes in a tree: additions, deletions,
renames and so on.

How do I stage and commit all of that?

git-commit -a

omits new files.

git-add .
git-commit -a

seemingly overlooks deletions.

What am I overlooking?  This should be simple, shouldn't it?

-- 
David Kastrup

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