You can use either an absolute path or a relative path. For relative paths, the current directory is usually PHP files. If you cannot access your scripts even with an absolute path, there may be a problem with access rights to the file system. Keep in mind that PHP scripts are usually executed as a web server (system) user account.
Your shell scripts should be stored somewhere close to or inside your application tree so that you can give them access to your PHP scripts (i.e. your web server), without compromising your file system security.
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