There are two ways to edit MySQL stopword list. Actually its not editing. Its all about creating a new file with your own stopwords & point MySQL to refer to that file location.
1st option
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Create File: e.g. /etc/stopword.txt
* Change permission of this file, so that MySQL can read it.
* Don't put stopword file in /root, because mysql doesn't have permission to access it there.
Edit /etc/my.cnf file
Search for ft_stopword_file
Change Line ft_stopword_file=/etc/stopword.txt
Then run following command to restart MySQL.
service mysqld restart
Run MySQL command, for immediate effect of this action on any table for Full-Text search.
REPAIR TABLE table_name QUICK;
2nd option
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You'll need to edit the file myisam/ft_static.c. recompile MySQL, and rebuild the indexes!
See the default list of full-text stopwords @
MySQL default stopwords list