✨ QD-10856 Create effective configuration in qodana cli

- in native mode (or in docker execution) effective configuration is created using `config-loader-cli.jar`, it's passed to linter and used for CLI
- in diff-start, diff-end mode, keep old behaviour (preserve bootstrap from new hash)
- refactor: separate QodanaYamlConfig objects for each context
- config-loader-cli.jar is downloaded by .sh script, verified using checksum file
- functions related to loading of qodana yaml now demonstrate that they don't load effective configuration
- tests

.github/workflows/ci.yml

@@ -27,6 +27,11 @@ jobs:
         with:
           cache-dependency-path: "**/*.sum"
           go-version-file: go.work
+      - name: Set up Java 17 for config-loader-cli.jar
+        uses: actions/setup-java@v3
+        with:
+          distribution: 'temurin' # Use the Temurin JDK distribution
+          java-version: '17'     # Java version 17
       - name: Overwrite tools (to run tests only on gh repo)
         run: |
           touch cdnet/clt.zip tooling/baseline-cli.jar tooling/intellij-report-converter.jar tooling/qodana-fuser.jar
@@ -45,6 +50,11 @@ jobs:
           )
           EOF
         shell: bash
+      - name: Download config-loader-cli.jar
+        run: |
+          chmod +x download_deps.sh
+          ./download_deps.sh
+        shell: bash
       - name: Set up gotestfmt
         uses: gotesttools/gotestfmt-action@v2
         with:

cdnet/options.go

@@ -42,27 +42,28 @@ func (l CdnetLinter) computeCdnetArgs(c thirdpartyscan.Context) ([]string, error
 		}
 		props += p
 	}
+	dotNet := c.QodanaYamlConfig().DotNet
 	if c.CdnetConfiguration() != "" {
 		if props != "" {
 			props += ";"
 		}
 		props += "Configuration=" + c.CdnetConfiguration()
-	} else if c.QodanaYaml().DotNet.Configuration != "" {
+	} else if dotNet.Configuration != "" {
 		if props != "" {
 			props += ";"
 		}
-		props += "Configuration=" + c.QodanaYaml().DotNet.Configuration
+		props += "Configuration=" + dotNet.Configuration
 	}
 	if c.CdnetPlatform() != "" {
 		if props != "" {
 			props += ";"
 		}
 		props += "Platform=" + c.CdnetPlatform()
-	} else if c.QodanaYaml().DotNet.Platform != "" {
+	} else if dotNet.Platform != "" {
 		if props != "" {
 			props += ";"
 		}
-		props += "Platform=" + c.QodanaYaml().DotNet.Platform
+		props += "Platform=" + dotNet.Platform
 	}
 	mountInfo := c.MountInfo()
 
@@ -94,8 +95,8 @@ func getSolutionOrProject(c thirdpartyscan.Context) string {
 	paths := [4]string{
 		c.CdnetSolution(),
 		c.CdnetProject(),
-		c.QodanaYaml().DotNet.Solution,
-		c.QodanaYaml().DotNet.Project,
+		c.QodanaYamlConfig().DotNet.Solution,
+		c.QodanaYamlConfig().DotNet.Project,
 	}
 	for _, path := range paths {
 		if path != "" {

cdnet/options_test.go

@@ -28,8 +28,8 @@ import (
 	"testing"
 )
 
-func createDefaultYaml(sln string, prj string, cfg string, plt string) qdyaml.QodanaYaml {
-	return qdyaml.QodanaYaml{
+func createDefaultYaml(sln string, prj string, cfg string, plt string) thirdpartyscan.QodanaYamlConfig {
+	return thirdpartyscan.QodanaYamlConfig{
 		DotNet: qdyaml.DotNet{
 			Solution:      sln,
 			Project:       prj,
@@ -49,20 +49,20 @@ func TestComputeCdnetArgs(t *testing.T) {
 		{
 			name: "No solution/project specified",
 			cb: thirdpartyscan.ContextBuilder{
-				Property:   []string{},
-				ResultsDir: "",
-				QodanaYaml: createDefaultYaml("", "", "", ""),
+				Property:         []string{},
+				ResultsDir:       "",
+				QodanaYamlConfig: createDefaultYaml("", "", "", ""),
 			},
 			expectedArgs: nil,
 			expectedErr:  "solution/project relative file path is not specified. Use --solution or --project flags or create qodana.yaml file with respective fields",
 		},
 		{
 			name: "project specified",
 			cb: thirdpartyscan.ContextBuilder{
-				Property:     []string{},
-				ResultsDir:   "",
-				CdnetProject: "project",
-				QodanaYaml:   createDefaultYaml("", "", "", ""),
+				Property:         []string{},
+				ResultsDir:       "",
+				CdnetProject:     "project",
+				QodanaYamlConfig: createDefaultYaml("", "", "", ""),
 			},
 			expectedArgs: []string{
 				"dotnet",
@@ -78,9 +78,9 @@ func TestComputeCdnetArgs(t *testing.T) {
 		{
 			name: "project specified in yaml",
 			cb: thirdpartyscan.ContextBuilder{
-				Property:   []string{},
-				ResultsDir: "",
-				QodanaYaml: createDefaultYaml("", "project", "", ""),
+				Property:         []string{},
+				ResultsDir:       "",
+				QodanaYamlConfig: createDefaultYaml("", "project", "", ""),
 			},
 			expectedArgs: []string{
 				"dotnet",
@@ -96,10 +96,10 @@ func TestComputeCdnetArgs(t *testing.T) {
 		{
 			name: "solution specified",
 			cb: thirdpartyscan.ContextBuilder{
-				Property:      []string{},
-				ResultsDir:    "",
-				CdnetSolution: "solution",
-				QodanaYaml:    createDefaultYaml("", "", "", ""),
+				Property:         []string{},
+				ResultsDir:       "",
+				CdnetSolution:    "solution",
+				QodanaYamlConfig: createDefaultYaml("", "", "", ""),
 			},
 			expectedArgs: []string{
 				"dotnet",
@@ -115,9 +115,9 @@ func TestComputeCdnetArgs(t *testing.T) {
 		{
 			name: "solution specified",
 			cb: thirdpartyscan.ContextBuilder{
-				Property:   []string{},
-				ResultsDir: "",
-				QodanaYaml: createDefaultYaml("solution", "", "", ""),
+				Property:         []string{},
+				ResultsDir:       "",
+				QodanaYamlConfig: createDefaultYaml("solution", "", "", ""),
 			},
 			expectedArgs: []string{
 				"dotnet",
@@ -133,9 +133,9 @@ func TestComputeCdnetArgs(t *testing.T) {
 		{
 			name: "configuration specified in yaml",
 			cb: thirdpartyscan.ContextBuilder{
-				Property:   []string{},
-				ResultsDir: "",
-				QodanaYaml: createDefaultYaml("solution", "", "cfg", ""),
+				Property:         []string{},
+				ResultsDir:       "",
+				QodanaYamlConfig: createDefaultYaml("solution", "", "cfg", ""),
 			},
 			expectedArgs: []string{
 				"dotnet",
@@ -155,7 +155,7 @@ func TestComputeCdnetArgs(t *testing.T) {
 				Property:           []string{},
 				ResultsDir:         "",
 				CdnetConfiguration: "cfg",
-				QodanaYaml:         createDefaultYaml("solution", "", "", ""),
+				QodanaYamlConfig:   createDefaultYaml("solution", "", "", ""),
 			},
 			expectedArgs: []string{
 				"dotnet",
@@ -172,9 +172,9 @@ func TestComputeCdnetArgs(t *testing.T) {
 		{
 			name: "platform specified in cfg",
 			cb: thirdpartyscan.ContextBuilder{
-				Property:   []string{},
-				ResultsDir: "",
-				QodanaYaml: createDefaultYaml("solution", "", "", "x64"),
+				Property:         []string{},
+				ResultsDir:       "",
+				QodanaYamlConfig: createDefaultYaml("solution", "", "", "x64"),
 			},
 			expectedArgs: []string{
 				"dotnet",
@@ -191,10 +191,10 @@ func TestComputeCdnetArgs(t *testing.T) {
 		{
 			name: "platform specified",
 			cb: thirdpartyscan.ContextBuilder{
-				Property:      []string{},
-				ResultsDir:    "",
-				CdnetPlatform: "x64",
-				QodanaYaml:    createDefaultYaml("solution", "", "", ""),
+				Property:         []string{},
+				ResultsDir:       "",
+				CdnetPlatform:    "x64",
+				QodanaYamlConfig: createDefaultYaml("solution", "", "", ""),
 			},
 			expectedArgs: []string{
 				"dotnet",
@@ -215,7 +215,7 @@ func TestComputeCdnetArgs(t *testing.T) {
 				ResultsDir:         "",
 				CdnetPlatform:      "x64",
 				CdnetConfiguration: "Debug",
-				QodanaYaml:         createDefaultYaml("solution", "", "", ""),
+				QodanaYamlConfig:   createDefaultYaml("solution", "", "", ""),
 			},
 			expectedArgs: []string{
 				"dotnet",
@@ -232,10 +232,10 @@ func TestComputeCdnetArgs(t *testing.T) {
 		{
 			name: "no-build",
 			cb: thirdpartyscan.ContextBuilder{
-				Property:     []string{},
-				ResultsDir:   "",
-				CdnetNoBuild: true,
-				QodanaYaml:   createDefaultYaml("solution", "", "", ""),
+				Property:         []string{},
+				ResultsDir:       "",
+				CdnetNoBuild:     true,
+				QodanaYamlConfig: createDefaultYaml("solution", "", "", ""),
 			},
 			expectedArgs: []string{
 				"dotnet",
@@ -261,8 +261,8 @@ func TestComputeCdnetArgs(t *testing.T) {
 					"idea.diagnostic.opentelemetry.file=/data/results/log/open-telemetry.json",
 					"jetbrains.security.package-checker.synchronizationTimeout=1000",
 				},
-				ResultsDir: "",
-				QodanaYaml: createDefaultYaml("solution", "", "", ""),
+				ResultsDir:       "",
+				QodanaYamlConfig: createDefaultYaml("solution", "", "", ""),
 			},
 			expectedArgs: []string{
 				"dotnet",

cdnet/run.go

@@ -39,7 +39,7 @@ func (l CdnetLinter) ComputeNewLinterInfo(
 }
 
 func (l CdnetLinter) RunAnalysis(c thirdpartyscan.Context) error {
-	utils.Bootstrap(c.QodanaYaml().Bootstrap, c.ProjectDir())
+	utils.Bootstrap(c.QodanaYamlConfig().Bootstrap, c.ProjectDir())
 	args, err := l.computeCdnetArgs(c)
 	if err != nil {
 		return err

cmd/cmd_test.go

@@ -149,13 +149,13 @@ func TestInitCommand(t *testing.T) {
 		t.Fatal(err)
 	}
 
-	filename := qdyaml.FindDefaultQodanaYaml(projectPath)
+	updatedQodanaYamlPath := qdyaml.GetLocalNotEffectiveQodanaYamlFullPath(projectPath, "")
 
-	if filename != "qodana.yml" {
-		t.Fatalf("expected \"qodana.yml\" got \"%s\"", filename)
+	if !strings.HasSuffix(updatedQodanaYamlPath, "qodana.yml") {
+		t.Fatalf("expected \"qodana.yml\" got \"%s\"", updatedQodanaYamlPath)
 	}
 
-	qodanaYaml := qdyaml.LoadQodanaYaml(projectPath, filename)
+	qodanaYaml := qdyaml.LoadQodanaYamlByFullPath(updatedQodanaYamlPath)
 
 	if qodanaYaml.Linter != product.Image(product.QDPY) {
 		t.Fatalf("expected \"%s\", but got %s", product.Image(product.QDPY), qodanaYaml.Linter)

cmd/init.go

@@ -38,8 +38,14 @@ func newInitCommand() *cobra.Command {
 		Short: "Configure a project for Qodana",
 		Long:  `Configure a project for Qodana: prepare Qodana configuration file by analyzing the project structure and generating a default configuration qodana.yaml file.`,
 		Run: func(cmd *cobra.Command, args []string) {
-			cliOptions.ConfigName = qdyaml.FindDefaultQodanaYaml(cliOptions.ProjectDir)
-			qodanaYaml := qdyaml.LoadQodanaYaml(cliOptions.ProjectDir, cliOptions.ConfigName)
+			localQodanaYamlFullPath := qdyaml.GetLocalNotEffectiveQodanaYamlFullPath(
+				cliOptions.ProjectDir,
+				cliOptions.ConfigName,
+			)
+			if localQodanaYamlFullPath == "" {
+				localQodanaYamlFullPath = filepath.Join(cliOptions.ProjectDir, "qodana.yaml")
+			}
+			qodanaYaml := qdyaml.LoadQodanaYamlByFullPath(localQodanaYamlFullPath)
 
 			ide := qodanaYaml.Ide
 			linter := qodanaYaml.Linter
@@ -61,9 +67,8 @@ func newInitCommand() *cobra.Command {
 				analyzer := commoncontext.GetAnalyzer(cliOptions.ProjectDir, token)
 
 				qdyaml.WriteQodanaLinterToYamlFile(
-					cliOptions.ProjectDir,
+					localQodanaYamlFullPath,
 					analyzer,
-					cliOptions.ConfigName,
 					product.AllCodes,
 				)
 				if product.IsNativeAnalyzer(analyzer) {
@@ -86,11 +91,11 @@ func newInitCommand() *cobra.Command {
 				)
 			}
 			if msg.IsInteractive() && qodanaYaml.IsDotNet() && (qodanaYaml.DotNet.IsEmpty() || cliOptions.Force) {
-				if commoncontext.GetAndSaveDotNetConfig(cliOptions.ProjectDir, cliOptions.ConfigName) {
+				if commoncontext.GetAndSaveDotNetConfig(cliOptions.ProjectDir, localQodanaYamlFullPath) {
 					msg.SuccessMessage("The .NET configuration was successfully set")
 				}
 			}
-			msg.PrintFile(filepath.Join(cliOptions.ProjectDir, cliOptions.ConfigName))
+			msg.PrintFile(localQodanaYamlFullPath)
 
 			commonCtx := commoncontext.Compute(
 				linter,

cmd/pull.go

@@ -21,7 +21,6 @@ import (
 	"github.com/JetBrains/qodana-cli/v2025/platform/commoncontext"
 	"github.com/JetBrains/qodana-cli/v2025/platform/qdcontainer"
 	"github.com/JetBrains/qodana-cli/v2025/platform/qdenv"
-	"github.com/JetBrains/qodana-cli/v2025/platform/qdyaml"
 	"github.com/docker/docker/client"
 	log "github.com/sirupsen/logrus"
 	"github.com/spf13/cobra"
@@ -36,10 +35,6 @@ func newPullCommand() *cobra.Command {
 		Short: "Pull latest version of linter",
 		Long:  `An alternative to pull an image.`,
 		Run: func(cmd *cobra.Command, args []string) {
-			if cliOptions.ConfigName == "" {
-				cliOptions.ConfigName = qdyaml.FindDefaultQodanaYaml(cliOptions.ProjectDir)
-			}
-
 			commonCtx := commoncontext.Compute(
 				cliOptions.Linter,
 				"",

cmd/scan.go

@@ -24,6 +24,7 @@ import (
 	"github.com/JetBrains/qodana-cli/v2025/platform"
 	"github.com/JetBrains/qodana-cli/v2025/platform/cmd"
 	"github.com/JetBrains/qodana-cli/v2025/platform/commoncontext"
+	"github.com/JetBrains/qodana-cli/v2025/platform/effectiveconfig"
 	"github.com/JetBrains/qodana-cli/v2025/platform/msg"
 	"github.com/JetBrains/qodana-cli/v2025/platform/qdenv"
 	"github.com/JetBrains/qodana-cli/v2025/platform/qdyaml"
@@ -50,8 +51,6 @@ But you can always override qodana.yaml options with the following command-line
 		Run: func(cmd *cobra.Command, args []string) {
 			ctx := cmd.Context()
 
-			qodanaYaml := qdyaml.LoadQodanaYaml(cliOptions.ProjectDir, cliOptions.ConfigName)
-
 			commonCtx := commoncontext.Compute(
 				cliOptions.Linter,
 				cliOptions.Ide,
@@ -67,7 +66,39 @@ But you can always override qodana.yaml options with the following command-line
 			checkProjectDir(commonCtx.ProjectDir)
 
 			preparedHost := startup.PrepareHost(commonCtx)
-			scanContext := corescan.CreateContext(*cliOptions, commonCtx, preparedHost, qodanaYaml)
+
+			effectiveConfigFiles := effectiveconfig.Files{}
+			qodanaYamlConfig := corescan.QodanaYamlConfig{}
+			if commonCtx.Ide != "" {
+				var err error
+				localQodanaYamlFullPath := qdyaml.GetLocalNotEffectiveQodanaYamlFullPath(
+					commonCtx.ProjectDir,
+					cliOptions.ConfigName,
+				)
+				effectiveConfigFiles, err = effectiveconfig.CreateEffectiveConfigFiles(
+					localQodanaYamlFullPath,
+					cliOptions.GlobalConfigurationsFile,
+					cliOptions.GlobalConfigurationId,
+					preparedHost.Prod.JbrJava(),
+					commonCtx.QodanaSystemDir,
+					"qdconfig",
+					commonCtx.LogDir(),
+				)
+				if err != nil {
+					log.Fatalf("Failed to load Qodana configuration %s", err)
+				}
+				if effectiveConfigFiles.EffectiveQodanaYamlPath != "" {
+					yaml := qdyaml.LoadQodanaYamlByFullPath(effectiveConfigFiles.EffectiveQodanaYamlPath)
+					qodanaYamlConfig = corescan.YamlConfig(yaml)
+				}
+			}
+			scanContext := corescan.CreateContext(
+				*cliOptions,
+				commonCtx,
+				preparedHost,
+				qodanaYamlConfig,
+				effectiveConfigFiles.ConfigDir,
+			)
 
 			exitCode := core.RunAnalysis(ctx, scanContext)
 			if qdenv.IsContainer() {