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All you will need to do is add your plugins to the plugins directory created by installing the nagios plugins package. This will ensure Nagios can reach, read, and execute the plugins if need be. Once they have been added to that directory you will need to define a command definition, then simply add that command definition to your host/service configs when creating them and they will use whatever you have defined there, please see the following for help defining commands:
I have download the checkMySQLProcesslist.sh file from this link https://github.com/tart/CheckMySQLProcesslist and copy to the libexec folder.
I have also give access rights to execute the file.
I don't know if it's just the file you sent is in an odd format, but the script isn't at all downloaded correctly.
I would recommend you copy the old one under a new name, and go the to link I sent in the last post and just copy and paste the code from there into a new file;
mv checkMySQLProcesslist.sh checkMySQLProcesslist-old.sh
vi checkMySQLProcesslist.sh
<paste in the new code, save and exit>
chmod a+x checkMySQLProcesslist.sh
chown nagios:nagios checkMySQLProcesslist.sh
Should look similar to that depending on your distro.