Ok, so just to clarify, this is what the file stucture should look like, right?
It certainly cut down on the number of errors and warnings, but I still get a bunch of occurances of the same problem as before but some of them went away.
Besides that, there is one thing I was hoping you could clarify for me. If I make a change with the tool, is it supposed to be changed in the actual mod files as well, or is there an additional step that I'm missing or something? Maybe it has something to do with how I load the files? I tried using the Import function originally, but it was tedious, and apparently no different from just copy/pasting. I suspect it probably has something to do with that, but I'm not really sure.
I use copy/paste and not the import/export to put files into the eclipse project sturcture. At it's core eclipse acts no differently from windows explorer and notepad when editing and saving files. The files are still accessible under your workspace and project directory even if eclipse is not running. You can also copy/paste from the Resource or Project explorer to windows explorer.
My validation tool doesn't actually modify any of your source files. What eclipse provides is a way to associate markers to source files that are displayed in the eclipse text editor. So if you save a file in eclipse the contents are saved to the harddrive like any other editor. You can then copy that file to the Sins mod directory for testing without worry.
Although, I would recommend looking at the build.xml and modifying the directories for your environment. The build.xml is a series of ant tasks with the purpose of automating deployment activities. This allows you to not modify files directly in the Sins mod directory or have to copy/paste entire mod files from your project to Sins mod directory. The ant tasks will validate if the file has changed and only copy it if needed. This applys to binary files such as textures as well.
Here is an example of the build.xml and the GameInfo files I used from your originally released mod to validate (left out the big stuff). With these files I only shows 2 errors and 74 warnings, most of this around PlayerPirate.entity missing references.
One of the errors was Description Resource Path Location Type invalid value! expected: [PerPlayer, ForAllPlayers]: buffStackingLimitType "Invalid" BuffDesignateTargetCaster.entity /Sot13T/Particle line 4 Entity Problem. This appears similar to the first several errors in your screenshot. I built the meta-definitions for the Entity validation from the core sins files and the value "Invalid" was used in very few places. I was hesistent to add this as an allowed value for other settings even though many mods make use it in different places. I can compromise though and make it a configurable option if needed (possibly to help when merging other mods which it appears may be the case with your screenshot).
The other error was a built-in buff type that doesn't actually relate to any buff entity file (BuffWormHoleTeleport).