I'd like to have a command-line interface (implemented as a .jar, runnable as java -jar $args rather than inside of, for example, Maven or Ant) that runs offline instrumentation on a certain set of input files, and which supports filtering based on fully-qualified classpath similar to InstrumentMojo.java

I'm planning on adding this functionality myself; I'm just opening this issue in case anyone can offer me some opinions about whether this sounds like a reasonable idea (probably the implementation is going to involve a new pom to build the cli jar and also adding some sort of filter into Instrumenter.java for distinguishing which files to instrument).