Remove files that are listed in the .gitignore but still on the repository.
git rm --cached file1 file2 dir/file3
Or, if you have a lot of files:
git rm --cached 'git ls-files -i --exclude-from=.gitignore'
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ActiveRecord::StatementInvalid (Mysql2::Error: SELECT list is not in GROUP BY clause and contains nonaggregated column which is not functionally dependent on columns in GROUP BY clause; this is incompatible with sql_mode=only_full_group_by):
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