I am trying to clean up a very very messy site that I took over from someone. It has thousands of unused files. I did this ....
Important: Although no other file in the site links to these files, some of the listed files may link to other files. Use caution when deleting the files.
My question is this. It great that it tells me that nothing links TO the file INCOMING but if it does not tell me if it links OUTGOING then how can I go ahead and delete it??
You should be able to save a report that you can look at in Excel, for instance, of your list of orphaned pages.
If, before you delete the pages, you also run a links report, one of the other report selections besides orphaned files, you will be able to see if there are links that you want to somehow preserve (perhaps by not deleting the pages until you have dealt with duplicating the links on live pages, if they warrant it).
Unfortunately or fortunately, this will not be a strictly mechanical operation, and you will get to know your site more intimately than you had previously expected, I imagine.
I sympathize with your clean-up duty. It is a thankless task (I hope you are getting paid to do it...), but it also leads to much vigilance on your part when you get to reworking the site.