How can I rewrite history so that all files, except the ones I already moved, are in a subdirectory?

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To rewrite the history with the files moved:

If you want the project’s history to look as though all files have always been in the directory foo/bar, then you need to do a little surgery. Use git filter-branch with the “tree filter” to rewrite the commits so that anywhere foo/bar doesn’t exist, it is created and all files are moved to it:

git filter-branch --prune-empty --tree-filter '
if [ ! -e foo/bar ]; then
    mkdir -p foo/bar
    git ls-tree --name-only $GIT_COMMIT | xargs -I files mv files foo/bar
fi'

Now the history will be recorded as if all files were always located in foo/bar.

To see the history of a moved file:

If you just want to see the history of a file that has been moved or renamed at some point in the past, then simply use the --follow option to git log:

git log --follow foo/bar/file.c

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