Breakpoints do not seem to be working now in the CLI. I went back to an earlier commit (94b2cc54412c2ebbfbaf3d4916f5591ce2f4b17c) and confirmed that they were working there.
This can be tested by running the following:
$ daffodil-cli/target/start -d parse -s daffodil-test/src/test/resources/edu/illinois/ncsa/daffodil/section06/entities/charClassEntities.dfdl.xsd -r matrix daffodil-cli/src/test/resources/edu/illinois/ncsa/daffodil/CLI/input/input2.txt
(debug) break element.cell
The debugger should show the breakpoint being hit by printing "breakpoint 1: element.cell".
Not sure if this is something test team should be fixing since it has to do with the CLI. If it is, feel free to assign back to me.