fix issue with analysis using tool configuration file

Author: DMarinhoCodacy

.codacy/codacy.yaml

@@ -27,8 +27,8 @@ go.work.sum
 # Codacy CLI 
 cli-v2
 codacy-cli
-**/.codacy/logs/
 .codacy/
+.github/instructions/
 
 
 #Ignore cursor AI rules

.gitignore

@@ -245,7 +245,7 @@ func loadsToolAndPatterns(toolName string, onlyEnabledPatterns bool) (domain.Too
 	}
 	var tool domain.Tool
 	for _, t := range toolsResponse {
-		if t.ShortName == toolName {
+		if t.Name == toolName {
 			tool = t
 			break
 		}
@@ -264,19 +264,19 @@ func getToolName(toolName string, version string) string {
 	if toolName == "eslint" {
 		switch majorVersion {
 		case 7:
-			return "eslint"
+			return "ESLint (deprecated)"
 		case 8:
-			return "eslint-8"
+			return "ESLint"
 		case 9:
-			return "eslint-9"
+			return "ESLint9"
 		}
 	} else {
 		if toolName == "pmd" {
 			switch majorVersion {
 			case 6:
-				return "pmd"
+				return "PMD"
 			case 7:
-				return "pmd-7"
+				return "PMD7"
 			}
 		}
 	}
@@ -351,10 +351,26 @@ func runToolByName(toolName string, workDirectory string, pathsToCheck []string,
 	if err != nil {
 		return err
 	}
+
+	// Get the tool name with the right version e.g. ESLint9, PMD7, etc.
+	toolRightVersion := getToolName(toolName, tool.Version)
+
+	// Get the repository tools to access tool settings
+	repositoryTools, _ := codacyclient.GetRepositoryTools(initFlags)
+
+	// Find the matching tool in repositoryTools
+	var t *domain.Tool
+	for i, tool := range repositoryTools {
+		if tool.Name == toolRightVersion {
+			t = &repositoryTools[i]
+			break
+		}
+	}
+
 	switch toolName {
 	case "eslint":
 		binaryPath := runtime.Binaries[tool.Runtime]
-		return tools.RunEslint(workDirectory, tool.InstallDir, binaryPath, pathsToCheck, autoFix, outputFile, outputFormat)
+		return tools.RunEslint(workDirectory, tool.InstallDir, binaryPath, pathsToCheck, autoFix, outputFile, outputFormat, t.Settings.UsesConfigurationFile)
 	case "trivy":
 		binaryPath := tool.Binaries[toolName]
 		return tools.RunTrivy(workDirectory, binaryPath, pathsToCheck, outputFile, outputFormat)

cmd/analyze.go

@@ -11,19 +11,21 @@ import (
 // * Run from the root of the repo we want to analyse
 // * NODE_PATH="<the installed eslint path>/node_modules"
 // * The local installed ESLint should have the @microsoft/eslint-formatter-sarif installed
-func RunEslint(repositoryToAnalyseDirectory string, eslintInstallationDirectory string, nodeBinary string, pathsToCheck []string, autoFix bool, outputFile string, outputFormat string) error {
+func RunEslint(repositoryToAnalyseDirectory string, eslintInstallationDirectory string, nodeBinary string, pathsToCheck []string, autoFix bool, outputFile string, outputFormat string, userUsesConfigurationFile bool) error {
 	eslintInstallationNodeModules := filepath.Join(eslintInstallationDirectory, "node_modules")
 	eslintJsPath := filepath.Join(eslintInstallationNodeModules, ".bin", "eslint")
 
 	cmd := exec.Command(nodeBinary, eslintJsPath)
 
 	// Add config file from tools-configs directory if it exists
-	if configFile, exists := ConfigFileExists(config.Config, "eslint.config.mjs"); exists {
-		// For Eslint compatibility with version 8.
-		// https://eslint.org/docs/v8.x/use/configure/configuration-files-new
-		cmd.Env = append(cmd.Env, "ESLINT_USE_FLAT_CONFIG=true")
+	if !userUsesConfigurationFile {
+		if configFile, exists := ConfigFileExists(config.Config, "eslint.config.mjs"); exists {
+			// For Eslint compatibility with version 8.
+			// https://eslint.org/docs/v8.x/use/configure/configuration-files-new
+			cmd.Env = append(cmd.Env, "ESLINT_USE_FLAT_CONFIG=true")
 
-		cmd.Args = append(cmd.Args, "-c", configFile)
+			cmd.Args = append(cmd.Args, "-c", configFile)
+		}
 	}
 
 	if autoFix {