Pass reverse-engineered business logic into migration/conversion pipeline (#45)

* Pass reverse-engineered business logic into migration/conversion pipeline

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

* feat: Enhance reverse engineering process with dependency mapping and business logic persistence

- Added dependency mapping step to ChunkedReverseEngineeringProcess and ReverseEngineeringProcess.
- Integrated IMigrationRepository for saving and reusing business logic and dependency maps.
- Updated RunMigrationAsync to support loading persisted business logic from previous runs with --reuse-re flag.
- Modified command-line interface to include options for reusing business logic and improved documentation.
- Enhanced README and architecture documentation to reflect changes in business logic persistence and usage.

* Fixing quality bots comments

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: jkordick <52427852+jkordick@users.noreply.github.com>
Co-authored-by: Julia Kordick <moin@jkordick.dev>

Author: Copilot

Agents/BusinessLogicExtractorAgent.cs

@@ -472,13 +472,19 @@ private List<FeatureDescription> ExtractFeatures(string analysisText, string fil
         {
             var line = lines[i].Trim();
 
-            if (line.StartsWith("###") && line.Contains("Feature", StringComparison.OrdinalIgnoreCase))
+            if (line.StartsWith("###") && (line.Contains("Feature", StringComparison.OrdinalIgnoreCase)
+                || line.Contains("Use Case", StringComparison.OrdinalIgnoreCase)
+                || line.Contains("Operation", StringComparison.OrdinalIgnoreCase)))
             {
                 if (currentFeature != null) features.Add(currentFeature);
                 currentFeature = new FeatureDescription
                 {
                     Id = $"F-{features.Count + 1}",
-                    Name = line.Replace("###", "").Replace("Feature:", "").Trim(),
+                    Name = System.Text.RegularExpressions.Regex.Replace(
+                        line.Replace("###", "").Trim(),
+                        @"^(Feature|Use Case \d+|Operation)[\s:]*",
+                        "",
+                        System.Text.RegularExpressions.RegexOptions.IgnoreCase).Trim(),
                     SourceLocation = fileName
                 };
             }

Agents/CSharpConverterAgent.cs

@@ -22,6 +22,7 @@ public class CSharpConverterAgent : AgentBase, ICodeConverterAgent
     public string FileExtension => ".cs";
 
     private int? _runId;
+    private List<BusinessLogic> _businessLogicExtracts = new();
 
     /// <summary>
     /// Sets the Run ID for the current context.
@@ -31,6 +32,12 @@ public void SetRunId(int runId)
         _runId = runId;
     }
 
+    /// <inheritdoc/>
+    public void SetBusinessLogicContext(List<BusinessLogic> businessLogicExtracts)
+    {
+        _businessLogicExtracts = businessLogicExtracts ?? new();
+    }
+
     /// <summary>
     /// Initializes a new instance using Responses API (for codex models like gpt-5.1-codex-mini).
     /// </summary>
@@ -107,7 +114,18 @@ public async Task<CodeFile> ConvertAsync(CobolFile cobolFile, CobolAnalysis cobo
             userPromptBuilder.AppendLine("Here is the analysis of the COBOL program:");
             userPromptBuilder.AppendLine();
             userPromptBuilder.AppendLine(cobolAnalysis.RawAnalysisData);
-            
+
+            // Inject business logic context from reverse engineering when available
+            var businessLogic = _businessLogicExtracts
+                .FirstOrDefault(bl => string.Equals(bl.FileName, cobolFile.FileName, StringComparison.OrdinalIgnoreCase));
+            if (businessLogic != null)
+            {
+                userPromptBuilder.AppendLine();
+                userPromptBuilder.AppendLine("Here is the extracted business logic from the reverse engineering phase. Use this to ensure the converted code faithfully implements all business rules and features:");
+                userPromptBuilder.AppendLine();
+                userPromptBuilder.Append(FormatBusinessLogicContext(businessLogic));
+            }
+
             userPromptBuilder.AppendLine();
             userPromptBuilder.AppendLine("IMPORTANT REQUIREMENTS:");
             userPromptBuilder.AppendLine("1. Return ONLY the C# code - NO explanations, NO markdown blocks");

Agents/ChunkAwareCSharpConverter.cs

@@ -18,6 +18,7 @@ public class ChunkAwareCSharpConverter : AgentBase, IChunkAwareConverter
 {
     private readonly ConversionSettings _conversionSettings;
     private int? _runId;
+    private List<BusinessLogic> _businessLogicExtracts = new();
 
     public string TargetLanguage => "CSharp";
     public string FileExtension => ".cs";
@@ -31,6 +32,12 @@ public void SetRunId(int runId)
         _runId = runId;
     }
 
+    /// <inheritdoc/>
+    public void SetBusinessLogicContext(List<BusinessLogic> businessLogicExtracts)
+    {
+        _businessLogicExtracts = businessLogicExtracts ?? new();
+    }
+
     /// <summary>
     /// Initializes a new instance using Responses API (for codex models like gpt-5.1-codex-mini).
     /// </summary>
@@ -384,6 +391,16 @@ private string BuildChunkAwareUserPrompt(ChunkResult chunk, ChunkContext context
             sb.AppendLine();
         }
 
+        // Inject business logic context from reverse engineering when available
+        var businessLogic = _businessLogicExtracts
+            .FirstOrDefault(bl => string.Equals(bl.FileName, chunk.SourceFile, StringComparison.OrdinalIgnoreCase));
+        if (businessLogic != null)
+        {
+            sb.AppendLine("Business logic context from reverse engineering (use to ensure accurate conversion):");
+            sb.AppendLine();
+            sb.Append(FormatBusinessLogicContext(businessLogic));
+        }
+
         sb.AppendLine("Return ONLY C# code. No markdown blocks. No explanations.");
 
         return sb.ToString();

Agents/ChunkAwareJavaConverter.cs

@@ -18,6 +18,7 @@ public class ChunkAwareJavaConverter : AgentBase, IChunkAwareConverter
 {
     private readonly ConversionSettings _conversionSettings;
     private int? _runId;
+    private List<BusinessLogic> _businessLogicExtracts = new();
 
     public string TargetLanguage => "Java";
     public string FileExtension => ".java";
@@ -31,6 +32,12 @@ public void SetRunId(int runId)
         _runId = runId;
     }
 
+    /// <inheritdoc/>
+    public void SetBusinessLogicContext(List<BusinessLogic> businessLogicExtracts)
+    {
+        _businessLogicExtracts = businessLogicExtracts ?? new();
+    }
+
     /// <summary>
     /// Initializes a new instance using Responses API (for codex models like gpt-5.1-codex-mini).
     /// </summary>
@@ -388,6 +395,16 @@ private string BuildChunkAwareUserPrompt(ChunkResult chunk, ChunkContext context
             sb.AppendLine();
         }
 
+        // Inject business logic context from reverse engineering when available
+        var businessLogic = _businessLogicExtracts
+            .FirstOrDefault(bl => string.Equals(bl.FileName, chunk.SourceFile, StringComparison.OrdinalIgnoreCase));
+        if (businessLogic != null)
+        {
+            sb.AppendLine("Business logic context from reverse engineering (use to ensure accurate conversion):");
+            sb.AppendLine();
+            sb.Append(FormatBusinessLogicContext(businessLogic));
+        }
+
         sb.AppendLine("Return ONLY Java code. No markdown blocks. No explanations.");
 
         return sb.ToString();

Agents/Infrastructure/AgentBase.cs

@@ -811,4 +811,57 @@ private string MergeAndValidateChunkOutputs(string part1, string part2, string c
 
         return merged;
     }
+
+    /// <summary>
+    /// Formats a <see cref="BusinessLogic"/> object as a concise text block suitable for injection
+    /// into AI conversion prompts. Shared by all converter agents.
+    /// </summary>
+    /// <param name="businessLogic">The business logic extracted during reverse engineering.</param>
+    /// <returns>A formatted string describing the business logic context.</returns>
+    protected static string FormatBusinessLogicContext(BusinessLogic businessLogic)
+    {
+        if (string.IsNullOrWhiteSpace(businessLogic.BusinessPurpose)
+            && businessLogic.BusinessRules.Count == 0
+            && businessLogic.Features.Count == 0
+            && businessLogic.UserStories.Count == 0)
+        {
+            return string.Empty;
+        }
+
+        var sb = new StringBuilder();
+        if (!string.IsNullOrWhiteSpace(businessLogic.BusinessPurpose))
+        {
+            sb.AppendLine($"Purpose: {businessLogic.BusinessPurpose}");
+        }
+        if (businessLogic.BusinessRules.Count > 0)
+        {
+            sb.AppendLine("Business Rules:");
+            foreach (var rule in businessLogic.BusinessRules)
+            {
+                sb.AppendLine($"- {rule.Description}");
+                if (!string.IsNullOrWhiteSpace(rule.Condition))
+                    sb.AppendLine($"  Condition: {rule.Condition}");
+                if (!string.IsNullOrWhiteSpace(rule.Action))
+                    sb.AppendLine($"  Action: {rule.Action}");
+            }
+        }
+        if (businessLogic.Features.Count > 0)
+        {
+            sb.AppendLine("Features:");
+            foreach (var feature in businessLogic.Features)
+            {
+                sb.AppendLine($"- {feature.Name}: {feature.Description}");
+            }
+        }
+        if (businessLogic.UserStories.Count > 0)
+        {
+            sb.AppendLine("Feature Descriptions:");
+            foreach (var story in businessLogic.UserStories)
+            {
+                sb.AppendLine($"- {story.Title}: {story.Action}");
+            }
+        }
+        sb.AppendLine();
+        return sb.ToString();
+    }
 }

Agents/Interfaces/ICodeConverterAgent.cs

@@ -38,4 +38,12 @@ public interface ICodeConverterAgent
     /// Sets the Run ID for the current context.
     /// </summary>
     void SetRunId(int runId);
+
+    /// <summary>
+    /// Sets the business logic context extracted during reverse engineering.
+    /// When provided, this context is injected into conversion prompts to guide
+    /// the AI in producing semantically accurate target code.
+    /// </summary>
+    /// <param name="businessLogicExtracts">Per-file business logic extracted during reverse engineering.</param>
+    void SetBusinessLogicContext(List<BusinessLogic> businessLogicExtracts);
 }

Agents/JavaConverterAgent.cs

@@ -22,6 +22,7 @@ public class JavaConverterAgent : AgentBase, IJavaConverterAgent, ICodeConverter
     public string FileExtension => ".java";
 
     private int? _runId;
+    private List<BusinessLogic> _businessLogicExtracts = new();
 
     /// <summary>
     /// Sets the Run ID for the current context.
@@ -31,6 +32,12 @@ public void SetRunId(int runId)
         _runId = runId;
     }
 
+    /// <inheritdoc/>
+    public void SetBusinessLogicContext(List<BusinessLogic> businessLogicExtracts)
+    {
+        _businessLogicExtracts = businessLogicExtracts ?? new();
+    }
+
     /// <summary>
     /// Initializes a new instance using Responses API (for codex models like gpt-5.1-codex-mini).
     /// </summary>
@@ -105,7 +112,18 @@ public async Task<JavaFile> ConvertToJavaAsync(CobolFile cobolFile, CobolAnalysi
             userPromptBuilder.AppendLine("Here is the analysis of the COBOL program to help you understand its structure:");
             userPromptBuilder.AppendLine();
             userPromptBuilder.AppendLine(cobolAnalysis.RawAnalysisData);
-            
+
+            // Inject business logic context from reverse engineering when available
+            var businessLogic = _businessLogicExtracts
+                .FirstOrDefault(bl => string.Equals(bl.FileName, cobolFile.FileName, StringComparison.OrdinalIgnoreCase));
+            if (businessLogic != null)
+            {
+                userPromptBuilder.AppendLine();
+                userPromptBuilder.AppendLine("Here is the extracted business logic from the reverse engineering phase. Use this to ensure the converted code faithfully implements all business rules and features:");
+                userPromptBuilder.AppendLine();
+                userPromptBuilder.Append(FormatBusinessLogicContext(businessLogic));
+            }
+
             userPromptBuilder.AppendLine();
             userPromptBuilder.AppendLine("IMPORTANT REQUIREMENTS:");
             userPromptBuilder.AppendLine("1. Return ONLY the Java code - NO explanations, NO markdown blocks, NO additional text");

CHANGELOG.md

@@ -5,6 +5,23 @@ All notable changes to this repository are documented here.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [2.5.0] - 2026-02-23
+
+### 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`.
+- **`--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.
+- **RE Results in Portal Chat** — Chat endpoint injects business purpose, user stories, features, and business rules from the `business_logic` table into the AI prompt context. Updated AI system prompt accordingly.
+
+### Fixed
+- **Empty Technical Analysis in RE output** — `ReverseEngineeringProcess` and `ChunkedReverseEngineeringProcess` now fall back to rendering `RawAnalysisData` when structured `CobolAnalysis` fields are unpopulated.
+- **Total Features always 0** — `BusinessLogicExtractorAgent.ExtractFeatures()` now matches `### Use Case N:` and `### Operation` headings in addition to `### Feature:`, reflecting the actual AI prompt output.
+
+### Changed
+- **Dependency mapping runs once per full run** — RE processes (`ReverseEngineeringProcess`, `ChunkedReverseEngineeringProcess`) now include a dedicated dependency mapping step (step 4/5) and store the result on `ReverseEngineeringResult.DependencyMap`. `MigrationProcess` and `ChunkedMigrationProcess` accept a `SetDependencyMap()` call and skip `AnalyzeDependenciesAsync` when a map is already provided. `SmartMigrationOrchestrator.RunAsync` threads `existingDependencyMap` through to both migration paths. Dependency output files (`dependency-map.json`, `dependency-diagram.md`) are now generated in the RE output folder as well as the migration output folder.
+- **`doctor.sh`** — Updated `convert-only` to prompt for `--reuse-re`; corrected portal navigation references to match current UI (`'📄 Reverse Engineering Results'`).
+
 ## [2.4.0] - 2026-02-16
 
 ### Added

Helpers/FileHelper.cs

@@ -429,6 +429,16 @@ private string ExtractClassNameFromContent(string content)
         return "GeneratedClass";
     }
 
+    /// <summary>Writes dependency-map.json and dependency-diagram.md to <paramref name="outputFolder"/>.</summary>
+    public async Task SaveDependencyOutputsAsync(DependencyMap dependencyMap, string outputFolder)
+    {
+        Directory.CreateDirectory(outputFolder);
+        await SaveDependencyMapAsync(dependencyMap, Path.Join(outputFolder, "dependency-map.json"));
+        await File.WriteAllTextAsync(
+            Path.Join(outputFolder, "dependency-diagram.md"),
+            $"# COBOL Dependency Diagram\n\n```mermaid\n{dependencyMap.MermaidDiagram}\n```");
+    }
+
     /// <summary>
     /// Saves a dependency map to disk as JSON.
     /// </summary>