docs: fill three documentation gaps from PR #45 (BL injection)

Co-authored-by: jkordick <52427852+jkordick@users.noreply.github.com>

Author: Copilot

CHANGELOG.md

@@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 - **Business Logic Persistence** — `ReverseEngineeringProcess` and `ChunkedReverseEngineeringProcess` now persist extracted `BusinessLogic` records to a new `business_logic` SQLite table via `IMigrationRepository.SaveBusinessLogicAsync`. Added `GetBusinessLogicAsync` and `DeleteBusinessLogicAsync` to `IMigrationRepository`, `SqliteMigrationRepository`, and `HybridMigrationRepository`.
+- **Business Logic Injection into Conversion Prompts** — All four converter agents (`JavaConverterAgent`, `CSharpConverterAgent`, `ChunkAwareJavaConverter`, `ChunkAwareCSharpConverter`) now receive extracted `BusinessLogic` records via `SetBusinessLogicContext()` (new method on `ICodeConverterAgent`). In full-pipeline runs, `SmartMigrationOrchestrator` wires RE output directly into conversion; `--reuse-re` loads the same context from a previous persisted RE run. A shared `FormatBusinessLogicContext()` helper in `AgentBase` formats the context for all four converters.
 - **`--reuse-re` CLI flag** — When combined with `--skip-reverse-engineering`, loads business logic from the latest persisted RE run and injects it into conversion prompts. `doctor.sh convert-only` now prompts interactively for this choice.
 - **REST API: `GET/DELETE /api/runs/{runId}/business-logic`** — Returns per-file business logic summary (story/feature/rule counts); DELETE removes persisted results to allow re-running RE for that run.
 - **Portal: per-run `🔬 RE Results` button** — Shows the business logic summary table for a run and allows deletion of persisted results directly from the UI.

README.md

@@ -791,12 +791,13 @@ sequenceDiagram
   BizLogic-->>RE: BusinessLogic[]
   RE->>Repo: persist analyses + documentation
   RE->>Repo: persist BusinessLogic[] to business_logic table
-  RE-->>CLI: ReverseEngineeringResult (with RunId)
+  RE-->>CLI: ReverseEngineeringResult (BusinessLogic[], RunId)
+  CLI->>Migration: SetBusinessLogicContext(BusinessLogic[])
   CLI->>Migration: start migration run with latest analyses
   Migration->>Analyzer: reuse or refresh CobolAnalysis
   Migration->>DepMap: build dependency graph (CALL/COPY/...)
   DepMap-->>Migration: DependencyMap
-  Migration->>Converter: convert to Java/C# (AI-limited concurrency)
+  Migration->>Converter: convert to Java/C# with business logic context
   Converter-->>Migration: CodeFile artifacts
   Migration->>Repo: persist run metadata, graph edges, code files
   Repo-->>Portal: expose MCP resources + REST APIs
@@ -838,6 +839,7 @@ sequenceDiagram
   - `CobolAnalysis` per file
   - Target language settings (Quarkus vs. .NET)
   - Migration run metadata (for logging & metrics)
+  - `BusinessLogic` records per file (user stories, features, business rules) — injected automatically from RE output in full-pipeline runs, or loaded from DB when `--reuse-re` is used
 - **Outputs:** `CodeFile` records saved under `output/java/` or `output/csharp/`.
 - **Interactions:**
   - Concurrency guards (pipeline slots vs. AI calls) ensure Azure OpenAI limits respected.