[scudlee]

I am a little confused at the instructions.

Do i simply install the repo and the moded ani db scapper thorough the repo and just add my sources?

Yes.

Or am i suppose to login to the anidb website and use this client java program in addition to the above?

Entirely optional. Using the client (with the renaming rules) just ensures everything is named perfectly for the scraper to be 100%(ish) accurate.

I get confused because of the following. Which implies i dont need to manually add the rules!?
 

New anime-list.xml
The scraper now uses my updated anime-list.xml by default. This list is significantly more complete the the old list, and being actively maintained. (Help very much welcome!)

This is unrelated. The mapping list is used by the scraper to provide episode plots and artwork from tvdb. It's not something you really need to be concerned with.

But there it continues to tell me to manually add the rules
[snip]
But what confuses me even more is after the following instructions, what am i suppose to do? just close out of the AniDB client and refresh my sources?

You'll first need to edit the BaseTVShowPath and BaseMoviePath variables to point to their respective folders, and you can also edit the FileInfo variable to however you like it.

If you look at the top two lines of the rules, you'll see two variables called "BaseTVShowPath" and "BaseMoviePath", change the values of them to be where you want your files to be placed.
After that you need to "add files" in the client and add all your anime files. The client will then run through the files and rename and sort them into one of those two locations (depending if it's a TV show or a movie).
Then you need to create an advancedsettings.xml (as explained in the first post) for Kodi to recognize the episode files.
Finally, in Kodi you set the folders you chose as source folders and use the TV scraper on the TV show path and the movie scraper on the movie path.
When you "acquire" new files, run them through the client to have them named and placed correctly, and then update your library in Kodi.

Again, this is all optional. It just ensures smooth running. Most anime files are not named in a fashion that Kodi will recognize without some form of intervention.