Currently most of the time is being spent in running the text of files through the obfuscator regular expressions. Files can instead be read and passed through the obfuscators in parallel. So the FileWalker should be modified that whenever it learns about a file it adds it to a queue which is picked up by a worker thread which processes the entire file.
Each worker should be initialized with all the same obfuscators as the FileWalker is currently.

We should also ensure that the obfuscators are threadsafe, particularly the replacement generation and lookup sections so ensure that for each value the replacement is generated only once.