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Which option should I choose when executing "i' (Ignore) on Magit? Should Gitignore be shared in private, at the top level or in subdirectory?

Top-level is the folder at the root of your git repo (probably .emacs.d in yr case). Choose t to write the ignores to .emacs.d/.gitignore which is probably what you want. But rather than hit i 37 ...
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How to force a git checkout revision in Magit if there are unstaged changes?

Do a hard reset first, if you want to discard the changes. M-x magit-reset-hard (X h) You can also do what is suggested, i.e. commit or stash.
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