The server file system should be configured so that the web server (e.g. Apache) does not have permission to edit or write the files which it then executes. That is, all of your files should be 'read only' for the Apache process, and owned with write permissions by a separate user.
For example, on many systems the Apache process runs as a user called "www-data" that is in a group called "www-data". This user should be able to read all of the files in your Drupal directory either by group permissions or by "other" permissions. It should not have write permissions to the code in your Drupal directory. If you use features of Drupal which require the "files" directory, then give the www-data user the permission to write files only in that directory.
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The server file system should be configured so that the web server