When running a CLI test using the debugger from a cygwin terminal the debugger seems to hang after any input. So after starting the debugger you see the (debug) prompt, type a command, hit enter, and then nothing ever happens. Also the debugger displays a warning that it is being used in a non interactive console which is not the case. This is not a problem when running in a windows command prompt.
This can be tested by running the following command on Windows in a cygwin terminal:
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/input1.txt