Refactor + tests (#6)

- Minor codebase clean-up
- Slight reorganisation of examples + tests so that we don't break stuff by accident
- CI tests

TESTING.md

@@ -0,0 +1,65 @@
+# Testing ReactICS
+
+## Prerequisites
+
+- **BDD module**: compiled (`./reactics setup` or `make` in `reactics-bdd/`)
+- **SMT module**: Python 3 with `z3-solver` and `pytest` installed
+
+```
+pip install z3-solver pytest
+```
+
+## Running all tests
+
+```
+./run_tests.sh
+```
+
+This runs the BDD, SMT, and generator test suites in sequence.
+
+## BDD tests
+
+```
+bash tests/run_tests.sh
+```
+
+10 regression tests that run the compiled `reactics-bdd/reactics` binary
+against example `.drs` files and compare output to saved baselines in
+`tests/expected/`. Covers:
+
+- Parsed system printing (`-P`)
+- Reaction listing (`-r`)
+- Reachable state enumeration (`-s`)
+- RSCTLK model checking (`-c`) for properties f1--f4
+
+Input files: `examples/bdd/tgc.drs`, `examples/bdd/tgc4.drs`,
+`reactics-bdd/in/trivial.drs`.
+
+To update baselines after an intentional output change, delete the
+relevant file in `tests/expected/` and re-run; the test will regenerate it.
+
+## SMT tests
+
+```
+python3 -m pytest tests/test_smt.py -v
+```
+
+23 pytest tests exercising the Python API directly. Organised by layer:
+
+- **Data model** -- ReactionSystem, concentrations, context automata,
+  formula construction (BagDescription, rsLTL)
+- **SmtCheckerRS** -- basic reachability (no concentrations)
+- **SmtCheckerRSC** -- reachability and rsLTL model checking with
+  concentrations (chain reaction, heat shock response)
+- **SmtCheckerRSCParam** -- parametric verification
+- **RSC-to-RS translation** -- verifying the translated system
+
+## Generator tests
+
+7 tests that run each generator (from `examples/bdd/generators/`),
+feed the output into the BDD model checker, and verify the expected
+verification result (holds / does not hold).
+
+Generators using old syntax (`examples/bdd/generators/old_syntax/`)
+are not tested this way as they are not compatible with the current
+parser.