Add config file support

.vscode/settings.json

@@ -0,0 +1,25 @@
+{
+	"editor.insertSpaces": false,
+	"editor.tabSize": 4,
+	"editor.detectIndentation": false,
+	"[csharp]": {
+		"editor.insertSpaces": false,
+		"editor.tabSize": 4
+	},
+	"[json]": {
+		"editor.insertSpaces": false,
+		"editor.tabSize": 2
+	},
+	"[xml]": {
+		"editor.insertSpaces": false,
+		"editor.tabSize": 2
+	},
+	"[yaml]": {
+		"editor.insertSpaces": true,
+		"editor.tabSize": 2
+	},
+	"[markdown]": {
+		"editor.insertSpaces": true,
+		"editor.tabSize": 2
+	}
+}

README.md

@@ -30,10 +30,15 @@ dotnet run -- --help
 
 ## 📖 Documentation
 
-- **User Guide:** `user-docs/cli_quick_reference.md`
-- **Docker Guide:** `user-docs/docker_usage.md`
-- **Technical Guide:** `doc/cli_skeleton_implementation.md`
-- **Architecture & Extension:** `doc/cli_architecture.md`
+### User Documentation
+- **CLI Quick Reference:** `user-docs/cli_quick_reference.md`
+- **Configuration Files:** `user-docs/configuration-files.md` - Batch analysis with JSON/YAML
+- **Docker Usage:** `user-docs/docker_usage.md`
+- **Vulnerability Scanning:** `user-docs/vulnerability-scanning.md`
+
+### Technical Documentation
+- **CLI Architecture:** `doc/cli_architecture.md`
+- **Implementation Guide:** `doc/cli_skeleton_implementation.md`
 - **Docker Implementation:** `doc/docker_implementation.md`
 - **Test Results:** `doc/cli_skeleton_test_results.md`
 
@@ -52,6 +57,7 @@ dotnet run -- --help
 - ✅ Multiple output formats (console, markdown)
 - ✅ Path argument support (`-p` / `--path`) for all analysis commands
 - ✅ Command-specific help with argument documentation
+- ✅ **Configuration file support (JSON & YAML) for batch analysis**
 
 ## 🎯 Current Commands
 
@@ -61,6 +67,11 @@ codemedic                # Show help (default)
 codemedic --help         # Explicit help
 codemedic --version      # Show version
 
+# Configuration-based batch analysis
+codemedic config <config-file>   # Run multiple analyses from config file
+codemedic config config.json
+codemedic config config.yaml
+
 # Analysis commands
 codemedic health         # Repository health dashboard
 codemedic health -p /path/to/repo --format markdown

run-config.cmd

@@ -0,0 +1,17 @@
+@echo off
+REM Run CodeMedic with a configuration file
+
+if "%1"=="" (
+    set CONFIG_FILE=sample-config.yaml
+) else (
+    set CONFIG_FILE=%1
+)
+
+if not exist "%CONFIG_FILE%" (
+    echo Configuration file not found: %CONFIG_FILE%
+    exit /b 1
+)
+
+echo Running CodeMedic with configuration: %CONFIG_FILE%
+
+dotnet run --project src\CodeMedic config %CONFIG_FILE%

run-config.ps1

@@ -0,0 +1,16 @@
+#!/usr/bin/env pwsh
+# Run CodeMedic with a configuration file
+
+param(
+    [Parameter(Mandatory=$false)]
+    [string]$ConfigFile = "sample-config.yaml"
+)
+
+if (-not (Test-Path $ConfigFile)) {
+    Write-Host "Configuration file not found: $ConfigFile" -ForegroundColor Red
+    exit 1
+}
+
+Write-Host "Running CodeMedic with configuration: $ConfigFile" -ForegroundColor Cyan
+
+dotnet run --project src\CodeMedic config $ConfigFile

run-config.sh

@@ -0,0 +1,13 @@
+#!/usr/bin/env bash
+# Run CodeMedic with a configuration file
+
+CONFIG_FILE="${1:-sample-config.yaml}"
+
+if [ ! -f "$CONFIG_FILE" ]; then
+    echo "Configuration file not found: $CONFIG_FILE"
+    exit 1
+fi
+
+echo "Running CodeMedic with configuration: $CONFIG_FILE"
+
+dotnet run --project src/CodeMedic config "$CONFIG_FILE"

sample-config-multi-repo.json

@@ -0,0 +1,23 @@
+{
+  "global": {
+    "format": "markdown",
+    "output-dir": "./reports/multi"
+  },
+  "repositories": [
+    {
+      "name": "MainProject",
+      "path": "./src",
+      "commands": ["health", "bom"]
+    },
+    {
+      "name": "TestSuite",
+      "path": "./test",
+      "commands": ["health"]
+    },
+    {
+      "name": "Documentation",
+      "path": "./docs",
+      "commands": ["bom"]
+    }
+  ]
+}

sample-config-multi-repo.yaml

@@ -0,0 +1,20 @@
+global:
+  format: markdown
+  output-dir: ./reports/multi
+
+repositories:
+  - name: MainProject
+    path: ./src
+    commands:
+      - health
+      - bom
+
+  - name: TestSuite
+    path: ./test
+    commands:
+      - health
+
+  - name: Documentation
+    path: ./docs
+    commands:
+      - bom

sample-config.json

@@ -0,0 +1,13 @@
+{
+  "global": {
+    "format": "markdown",
+    "output-dir": "./reports"
+  },
+  "repositories": [
+    {
+      "name": "CodeMedic",
+      "path": ".",
+      "commands": ["health", "bom", "vulnerabilities"]
+    }
+  ]
+}

sample-config.yaml

@@ -0,0 +1,11 @@
+global:
+  format: markdown
+  output-dir: ./reports
+
+repositories:
+  - name: CodeMedic
+    path: .
+    commands:
+      - health
+      - bom
+      - vulnerabilities

src/CodeMedic/CodeMedic.csproj

@@ -34,6 +34,7 @@
     </PackageReference>
     <PackageReference Include="System.CommandLine" Version="2.0.0" />
     <PackageReference Include="Spectre.Console" Version="0.49.1" />
+    <PackageReference Include="YamlDotNet" Version="16.3.0" />
   </ItemGroup>
 
   <ItemGroup>

src/CodeMedic/Commands/ConfigurationCommandHandler.cs

@@ -0,0 +1,145 @@
+using CodeMedic.Utilities;
+using CodeMedic.Commands;
+using CodeMedic.Output;
+
+namespace CodeMedic.Commands;
+
+/// <summary>
+/// Handles configuration-related commands.
+/// </summary>
+public class ConfigurationCommandHandler
+{
+	private PluginLoader _PluginLoader;
+
+	/// <summary>
+	/// Initializes a new instance of the <see cref="ConfigurationCommandHandler"/> class.
+	/// </summary>
+	/// <param name="pluginLoader">The plugin loader instance used to manage plugins.</param>
+	public ConfigurationCommandHandler(PluginLoader pluginLoader)
+	{
+		_PluginLoader = pluginLoader;
+	}
+
+	/// <summary>
+	/// Handles the configuration file command.
+	/// </summary>
+	/// <param name="configFilePath">The path to the configuration file.</param>
+	/// <returns>A task that represents the asynchronous operation. The task result contains the exit code.</returns>
+	internal async Task<int> HandleConfigurationFileAsync(string configFilePath)
+	{
+
+		// Check if the configuration file exists
+		if (!File.Exists(configFilePath))
+		{
+			RootCommandHandler.Console.RenderError($"Configuration file not found: {configFilePath}");
+			return 1; // Return a non-zero exit code to indicate failure
+		}
+
+		// Load the specified configuration file - we need to identify the file type and load accordingly
+		CodeMedicRunConfiguration config;
+		try {
+		config = LoadConfigurationFromFile(configFilePath);
+		if (config == null)
+		{
+			RootCommandHandler.Console.RenderError($"Failed to load configuration from file: {configFilePath}");
+			return 1; // Return a non-zero exit code to indicate failure
+		}
+		} catch (Exception ex)
+		{
+			RootCommandHandler.Console.RenderError($"Error loading configuration file: {ex.Message}");
+			return 1; // Return a non-zero exit code to indicate failure
+		}
+
+		await RunCommandsForConfigurationAsync(config);
+
+		return 0; // Return zero to indicate success
+
+	}
+
+	private async Task RunCommandsForConfigurationAsync(CodeMedicRunConfiguration config)
+	{
+
+		// For each repository in the configuration, run the specified commands
+		foreach (var repoConfig in config.Repositories)
+		{
+			RootCommandHandler.Console.RenderInfo($"Processing repository: {repoConfig.Name} at {repoConfig.Path}");
+
+			foreach (var commandName in repoConfig.Commands)
+			{
+
+				// Check that the command is registered with the plugin loader
+				if (!_PluginLoader.Commands.ContainsKey(commandName))
+				{
+					RootCommandHandler.Console.RenderError($"  Command not registered: {commandName}");
+					continue;
+				}
+
+				RootCommandHandler.Console.RenderInfo($"  Running command: {commandName}");
+
+				// Load the command plugin
+				var commandPlugin = _PluginLoader.GetCommand(commandName);
+				if (commandPlugin == null)
+				{
+					RootCommandHandler.Console.RenderError($"    Command plugin not found: {commandName}");
+					continue;
+				}
+
+				// Get the Formatter plugin for output formatting - we only support markdown for now
+				// Ensure output directory exists
+				Directory.CreateDirectory(config.Global.OutputDirectory);
+
+				var reportPath = Path.Combine(config.Global.OutputDirectory, $"{repoConfig.Name}_{commandName}.md");
+
+				// Execute the command with proper disposal of the StreamWriter
+				using (var writer = new StreamWriter(reportPath))
+				{
+					var formatter = new MarkdownRenderer(writer);
+
+					// Build arguments array to pass the repository path to the command
+					var commandArgs = new[] { "--path", repoConfig.Path };
+
+					await commandPlugin.Handler(commandArgs, formatter);
+				}
+
+			}
+			// For now, just simulate with a delay
+			await Task.Delay(500);
+
+			RootCommandHandler.Console.RenderInfo($"Completed processing repository: {repoConfig.Name}");
+		}
+
+	}
+
+	private CodeMedicRunConfiguration LoadConfigurationFromFile(string configFilePath)
+	{
+		// detect if the file is json or yaml based on extension
+		var extension = Path.GetExtension(configFilePath).ToLower();
+		var fileContents = File.ReadAllText(configFilePath);
+		if (extension == ".json")
+		{
+			var config = System.Text.Json.JsonSerializer.Deserialize<CodeMedicRunConfiguration>(fileContents);
+			if (config == null)
+			{
+				throw new InvalidOperationException("Failed to deserialize JSON configuration file.");
+			}
+			return config;
+		}
+		else if (extension == ".yaml" || extension == ".yml")
+		{
+			// Configure YAML deserializer - we use explicit YamlMember aliases on properties
+			var deserializer = new YamlDotNet.Serialization.DeserializerBuilder()
+				.Build();
+			var config = deserializer.Deserialize<CodeMedicRunConfiguration>(fileContents);
+			if (config == null)
+			{
+				throw new InvalidOperationException("Failed to deserialize YAML configuration file.");
+			}
+			return config;
+		}
+		else
+		{
+			throw new InvalidOperationException("Unsupported configuration file format. Only JSON and YAML are supported.");
+		}
+	}
+
+}