Make Git automatically remove trailing white space before committing

Those settings (core.whitespace and apply.whitespace) are not there to remove trailing whitespace but to:

• core.whitespace: detect them, and raise errors
• apply.whitespace: and strip them, but only during patch, not “always automatically”

I believe the git hook pre-commit would do a better job for that (includes removing trailing whitespace)

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Note that at any given time you can choose to not run the pre-commit hook:

• temporarily: git commit --no-verify .
• permanently: cd .git/hooks/ ; chmod -x pre-commit

Warning: by default, a pre-commit script (like this one), has not a “remove trailing” feature”, but a “warning” feature like:

if (/\s$/) {
    bad_line("trailing whitespace", $_);
}

You could however build a better pre-commit hook, especially when you consider that:

Committing in Git with only some changes added to the staging area still results in an “atomic” revision that may never have existed as a working copy and may not work.

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For instance, oldman proposes in another answer a pre-commit hook which detects and remove whitespace.
Since that hook get the file name of each file, I would recommend to be careful for certain type of files: you don’t want to remove trailing whitespace in .md (markdown) files!

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Another approach, suggested by hakre in the comments:

You can have two spaces at end of line in markdown and not have it as trailing whitespace by adding “\” before \n.

Then a content filter driver:

git config --global filter.space-removal-at-eol.clean 'sed -e "s/ \+$//"'
# register in .gitattributes 
*.md filter=space-removal-at-eol