Background: I was recently making a Drupal site where I needed (as is often the case) a visual text editor along with image- and file-upload capabilities. I tried using the wysiwyg module in conjunction FCKEditor 2.6.x, which is a good combination for that purpose.
Since this does not work out of the box, I followed the instructions here.
This procedure requires modifying files in the Wysiwyg module (residing in sites/all/modules) as well as the FCKEditor library itself (in sites/all/libraries).
The causes potential problems when the module and library are upgraded. My solution is to use patches. Here is how.
diff -cr sites/all/modules/wysiwyg/ sites/all/modules/wysiwyg.patched/ > patches/wysiwyg_module_allow_file_uploads.diff
patch -p0 < patches/wysiwyg_module_allow_file_uploads.diff
(note: I sometimes use the IMCE module to integrate image uploading with visual editors, which does not require any patching. In this case it was decided to use upload capabilities already integrated into FCKEditor because it is easier for the end user.)