Document state accounting in API and output docs

Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)

Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>

Author: oceanusXXD

docs/output-layout.md

@@ -39,6 +39,8 @@ Within this bundle, `code2skill` treats generated Skills as the final product la
 - `references/*.md`: supporting architectural and workflow references
 - `state/analysis-state.json`: incremental execution cache
 
+When `write_state` is enabled, both `report.json` accounting and `ScanExecution.output_files` include `state/analysis-state.json` in this intermediate layer.
+
 In product terms, `.code2skill/` is the workspace-local artifact bundle. The final repository-local product is the generated Skill set, while `adapt` publishes that Skill layer into the repository locations where each AI tool expects to read it.
 
 ## Adapted Outputs

docs/python-api.md

@@ -76,6 +76,8 @@ The pipeline functions return `ScanExecution`, which includes:
 - `report_path`
 - `report`
 
+When state persistence is enabled, `output_files` includes the state snapshot path as part of the written intermediate artifact set.
+
 The embedded `ExecutionReport` also distinguishes between:
 
 - `final_product_files`: the generated Skill artifacts inside the bundle