diff --git a/libraries/analysis-javascript/lib/RootContext.ts b/libraries/analysis-javascript/lib/RootContext.ts
index 119a2d338..986b1daca 100644
--- a/libraries/analysis-javascript/lib/RootContext.ts
+++ b/libraries/analysis-javascript/lib/RootContext.ts
@@ -27,7 +27,7 @@ import { DependencyFactory } from "./dependency/DependencyFactory";
 import { Export } from "./target/export/Export";
 import { TargetFactory } from "./target/TargetFactory";
 import { TypeModelFactory } from "./type/resolving/TypeModelFactory";
-import { getAllFiles, readFile } from "./utils/fileSystem";
+import { readFile } from "./utils/fileSystem";
 import { ExportFactory } from "./target/export/ExportFactory";
 import { TypeExtractor } from "./type/discovery/TypeExtractor";
 import { TypeModel } from "./type/resolving/TypeModel";
@@ -51,7 +51,9 @@ export class RootContext extends CoreRootContext<t.Node> {
 
   protected _constantPoolFactory: ConstantPoolFactory;
 
-  protected _files: string[];
+  protected _targetFiles: Set<string>;
+  protected _analysisFiles: Set<string>;
+
   // filepath -> id -> element
   protected _elementMap: Map<string, Map<string, Element>>;
   // filepath -> id -> relation
@@ -67,6 +69,8 @@ export class RootContext extends CoreRootContext<t.Node> {
 
   constructor(
     rootPath: string,
+    targetFiles: Set<string>,
+    analysisFiles: Set<string>,
     abstractSyntaxTreeFactory: AbstractSyntaxTreeFactory,
     controlFlowGraphFactory: ControlFlowGraphFactory,
     targetFactory: TargetFactory,
@@ -85,6 +89,8 @@ export class RootContext extends CoreRootContext<t.Node> {
       dependencyFactory
     );
     RootContext.LOGGER = getLogger("RootContext");
+    this._targetFiles = targetFiles;
+    this._analysisFiles = analysisFiles;
     this._exportFactory = exportFactory;
     this._typeExtractor = typeExtractor;
     this._typeResolver = typeResolver;
@@ -95,21 +101,6 @@ export class RootContext extends CoreRootContext<t.Node> {
     return this._rootPath;
   }
 
-  // TODO something with the types
-
-  getFiles() {
-    if (!this._files) {
-      this._files = getAllFiles(this.rootPath, ".js").filter(
-        (x) =>
-          !x.includes("/test/") &&
-          !x.includes(".test.js") &&
-          !x.includes("node_modules")
-      ); // maybe we should also take those into account
-    }
-
-    return this._files;
-  }
-
   override getSource(filePath: string) {
     let absoluteTargetPath = this.resolvePath(filePath);
 
@@ -172,7 +163,7 @@ export class RootContext extends CoreRootContext<t.Node> {
     if (!this._exportMap) {
       this._exportMap = new Map();
 
-      for (const filepath of this.getFiles()) {
+      for (const filepath of this._analysisFiles) {
         this._exportMap.set(filepath, this.getExports(filepath));
       }
     }
@@ -208,7 +199,7 @@ export class RootContext extends CoreRootContext<t.Node> {
     if (!this._elementMap) {
       this._elementMap = new Map();
 
-      for (const filepath of this.getFiles()) {
+      for (const filepath of this._analysisFiles) {
         this._elementMap.set(filepath, this.getElements(filepath));
       }
     }
@@ -244,7 +235,7 @@ export class RootContext extends CoreRootContext<t.Node> {
     if (!this._relationMap) {
       this._relationMap = new Map();
 
-      for (const filepath of this.getFiles()) {
+      for (const filepath of this._analysisFiles) {
         this._relationMap.set(filepath, this.getRelations(filepath));
       }
     }
@@ -280,7 +271,7 @@ export class RootContext extends CoreRootContext<t.Node> {
     if (!this._objectMap) {
       this._objectMap = new Map();
 
-      for (const filepath of this.getFiles()) {
+      for (const filepath of this._analysisFiles) {
         this._objectMap.set(filepath, this.getObjectTypes(filepath));
       }
     }
@@ -332,7 +323,7 @@ export class RootContext extends CoreRootContext<t.Node> {
   // TODO cache
   private _getContextConstantPool(): ConstantPool {
     const constantPool = new ConstantPool();
-    for (const filepath of this.getFiles()) {
+    for (const filepath of this._analysisFiles) {
       const ast = this.getAbstractSyntaxTree(filepath);
       this._constantPoolFactory.extract(filepath, ast, constantPool);
     }
diff --git a/tools/javascript/lib/JavaScriptLauncher.ts b/tools/javascript/lib/JavaScriptLauncher.ts
index 107718571..de4be0f1b 100644
--- a/tools/javascript/lib/JavaScriptLauncher.ts
+++ b/tools/javascript/lib/JavaScriptLauncher.ts
@@ -44,6 +44,7 @@ import {
   ProcreationPlugin,
   TerminationTriggerPlugin,
   PropertyName,
+  FileSelector,
 } from "@syntest/base-language";
 import {
   UserInterface,
@@ -170,8 +171,35 @@ export class JavaScriptLauncher extends Launcher {
       (<JavaScriptArguments>this.arguments_).syntaxForgiving
     );
 
+    const fileSelector = new FileSelector();
+    const targetFiles = fileSelector.loadFilePaths(
+      this.arguments_.targetInclude,
+      this.arguments_.targetExclude
+    );
+
+    if (this.arguments_.analysisInclude.length === 0) {
+      JavaScriptLauncher.LOGGER.warn(
+        "'analysis-include' config parameter is empty so we only use the target files for analysis"
+      );
+    }
+
+    for (const target of targetFiles) {
+      if (this.arguments_.analysisExclude.includes(target)) {
+        throw new Error(
+          `Target files cannot be excluded from analysis. Target file: ${target}`
+        );
+      }
+    }
+
+    const analysisFiles = fileSelector.loadFilePaths(
+      [...targetFiles, ...this.arguments_.analysisInclude],
+      this.arguments_.analysisExclude
+    );
+
     this.rootContext = new RootContext(
       this.arguments_.targetRootDirectory,
+      targetFiles,
+      analysisFiles,
       abstractSyntaxTreeFactory,
       controlFlowGraphFactory,
       targetFactory,
@@ -184,15 +212,6 @@ export class JavaScriptLauncher extends Launcher {
 
     this.userInterface.printHeader("GENERAL INFO");
 
-    // TODO ui info messages
-
-    // this.userInterface.report("property-set", [
-    //   "Target Settings",
-    //   <string>(
-    //     (<unknown>[["Target Root Directory", this.arguments_.targetRootDirectory]])
-    //   ),
-    // ]);
-
     const timeInMs = (Date.now() - start) / 1000;
     this.metricManager.recordProperty(
       PropertyName.INITIALIZATION_TIME,
@@ -209,8 +228,8 @@ export class JavaScriptLauncher extends Launcher {
     const startTargetSelection = Date.now();
     const targetSelector = new TargetSelector(this.rootContext);
     this.targets = targetSelector.loadTargets(
-      this.arguments_.include,
-      this.arguments_.exclude
+      this.arguments_.targetInclude,
+      this.arguments_.targetExclude
     );
     let timeInMs = (Date.now() - startTargetSelection) / 1000;
     this.metricManager.recordProperty(
@@ -221,7 +240,7 @@ export class JavaScriptLauncher extends Launcher {
     if (this.targets.length === 0) {
       // Shut server down
       this.userInterface.printError(
-        `No targets where selected! Try changing the 'include' parameter`
+        `No targets where selected! Try changing the 'target-include' parameter`
       );
       await this.exit();
       // eslint-disable-next-line unicorn/no-process-exit
@@ -243,6 +262,19 @@ export class JavaScriptLauncher extends Launcher {
 
     this.userInterface.printItemization("TARGETS", itemization);
 
+    const selectionSettings: TableObject = {
+      headers: ["Setting", "Value"],
+      rows: [
+        ["Target Root Directory", this.arguments_.targetRootDirectory],
+        ["Target Include", `${this.arguments_.targetInclude.join(", ")}`],
+        ["Target Exclude", `${this.arguments_.targetExclude.join(", ")}`],
+        ["Analysis Include", `${this.arguments_.analysisInclude.join(", ")}`],
+        ["Analysis Exclude", `${this.arguments_.analysisExclude.join(", ")}`],
+      ],
+      footers: ["", ""],
+    };
+    this.userInterface.printTable("SELECTION SETTINGS", selectionSettings);
+
     const settings: TableObject = {
       headers: ["Setting", "Value"],
       rows: [