refactor: store runtime objects in domain

phases/domain-runtime-storage/step3.md

@@ -0,0 +1,42 @@
+# Step 3: step-and-set-runtime-references
+
+## Read First
+
+Read these files before editing:
+
+- `/AGENTS.md`
+- `/docs/AGENT_RULES.md`
+- `/docs/implementation-plans/domain-runtime-storage-implementation-plan.md`
+- `/include/fesa/core/Domain.hpp`
+- `/include/fesa/core/StepDefinition.hpp`
+- `/src/core/Domain.cpp`
+- `/tests/core/domain_storage_test.cpp`
+
+## Task
+
+Make Domain set and step validation reference runtime storage.
+
+Rules:
+
+- `Domain::addElementSet` must validate ids against runtime elements stored by `Domain::findElement`.
+- `Domain::addStep(LinearStaticStepDefinition)` may remain for now, but its boundary and load indices must validate against runtime boundary and load containers.
+- Failed insertions must not mutate Domain counts.
+- No equation ids, solver vectors, residuals, reactions, current time, or iteration state may be added to Domain.
+
+## Tests To Write First
+
+- Rewrite `/tests/core/domain_storage_test.cpp` set and step tests so they build elements, loads, and boundary conditions through runtime object APIs.
+- Preserve count-stability tests for failed insertions.
+
+## Acceptance Criteria
+
+```powershell
+ctest --test-dir build/msvc-debug --output-on-failure -C Debug -R domain
+python scripts/validate_workspace.py
+```
+
+## Verification Notes
+
+1. Run targeted CTest before production edits and confirm failure.
+2. Keep `LinearStaticStepDefinition` as the only remaining step record until a separate step-model phase exists.
+3. Update `phases/domain-runtime-storage/index.json` for this step result.