Did you do these changes automatically or did you first manually look at each? All the changes in other classes look fine apart from: ArdenBaseTreeParser.java
Some of the changes there may introduce bugs.
Because of this: "Note that Sun's javac compiler often generates dead stores for final local variables. Because FindBugs is a bytecode-based tool, there is no easy way to eliminate these false positives", i feel like we should not automate this in particular. We need to manually look at each one by one. :)

Here is an example: http://stackoverflow.com/questions/17781768/sonar-dead-store-to-local-variable

@lrozanski am ok with all other changes save the ones in the file "ArdenBaseTreeParser.java"
This requires a manual inspection for each line you want to change (instead of the automated one) because of its complexity and the possibility of false positives which could introduce bugs.

All of the lines I deleted were never used anywhere else and only had one occurrence. They were safe to delete.

Let me put it this way, when it comes to this particular class, which has lots of deletions, did you do them manually one by one? Or automated it?

I have not deleted a single line automatically, from any file. All of the changes I made were done manually, and I checked each line in question for this particular class before deleting anything.