Document the SBOL provenance model

ARCHITECTURE.md

@@ -482,6 +482,8 @@ Responsibilities:
 
 ## SBOL assembly service
 
+The [SBOL provenance guide](docs/sbol_provenance.rst) documents the implemented entity/activity/agent relationships, stage differences, document ownership, and export limitations. Use it when interpreting or extending SBOL build artifacts.
+
 Port the current working `Assembly` behavior mostly intact into `sbol/assembly.py`, behind a cleaner service interface. Refactor internals only after tests protect the new contract.
 
 ```python

README.md

@@ -16,6 +16,8 @@ abstract SBOL design + inventory -> build plan -> SBOL build artifacts -> PUDU J
 
 The Read the Docs site is available at [buildcompiler.readthedocs.io](https://buildcompiler.readthedocs.io/en/latest/) and is built from the Sphinx documentation in `docs/`.
 
+The [SBOL provenance guide](docs/sbol_provenance.rst) explains how biological entities, activities, agents, plans, and generated results are connected, including stage coverage, graph traversal, and the distinction between compiler records and physical execution.
+
 The compiler should answer:
 
 - Can this design be built from current inventory?

docs/index.rst

@@ -43,6 +43,7 @@ Representative use cases
 
    installation
    quickstart
+   sbol_provenance
    examples/offline_lvl1
    examples/transformation_pudu
    examples/full_build