Many people with some knowledge of php meets a problem with wordpress - then tries to find their way in the core code - they find a solution as a hack. This is known as the bad solution of course, but I guess many plugin writers also come this way, before they write the actual plugin.
If you not are familiar with wordpress and mayby not want to dive into wordpress, it can take many hours to find the right hook and getting to work what the hack makes.
My suggestion is that if you place a file with for example the name link-template.php in your theme folder, then wordpress will use that file instead of the file located in wp-includes. All it will take is that all wordpress core files have unique names and a htacces that does the job. Of course only meant as an alternative to filters and hooks. I dont see any difficulties in it, but mayby I am wrong?