Add note regarding JSON output. [ci skip]

Author: lohedges

README.md

@@ -101,7 +101,10 @@ stream file for the perturbable molecule, or AMBER or GROMACS files for the two
 The format can be specified using the the `--output-format` option. If you require input
 for a free-energy perturbation simulation, e.g. a hybrid GROMACS toplogy file, the you can
 use the stream file with [BioSimSpace](https://biosimspace.openbiosim.org) to generate the
-required input files.
+required input files. Additionally, the program will output a JSON file summarising the
+modifications that were made.
+
+```bash
 
 > [!NOTE]
 > When a stream file is used as input, the `--mapping` option is ignored. and