@harness-engineering/cli 1.25.6 → 1.25.7

package/dist/{chunk-SMY35HJM.js → chunk-JPZY7ZQX.js}

@@ -15,7 +15,7 @@ function evictIfNeeded() {
   }
 }
 async function doLoadGraphStore(projectRoot) {
-  const { GraphStore } = await import("./dist-GRW3X2ZQ.js");
+  const { GraphStore } = await import("./dist-HPWNWCT6.js");
   const graphDir = path.join(projectRoot, ".harness", "graph");
   const store = new GraphStore();
   const loaded = await store.load(graphDir);

package/dist/{chunk-FL6A72LV.js → chunk-K35D7HF3.js}

@@ -3,7 +3,7 @@ import {
 } from "./chunk-KET4QQZB.js";
 import {
   init_dist
-} from "./chunk-42ZZLMYD.js";
+} from "./chunk-ZIYLIYN4.js";
 import {
   Err,
   Ok

package/dist/{chunk-BUJOMC3O.js → chunk-K533WNZG.js}

@@ -1,6 +1,6 @@
 import {
   init_dist
-} from "./chunk-42ZZLMYD.js";
+} from "./chunk-ZIYLIYN4.js";
 import {
   Err,
   Ok
@@ -84,7 +84,33 @@ function mergePackageJson(base, overlay) {
 }
 
 // src/templates/engine.ts
-var NON_JSON_PACKAGE_CONFIGS = /* @__PURE__ */ new Set(["pyproject.toml", "go.mod", "Cargo.toml", "pom.xml"]);
+var NON_JSON_PACKAGE_CONFIGS = /* @__PURE__ */ new Set([
+  "pyproject.toml",
+  "go.mod",
+  "Cargo.toml",
+  "pom.xml",
+  "build.gradle",
+  "build.gradle.kts"
+]);
+var HARNESS_CONFIG_FILES = /* @__PURE__ */ new Set(["harness.config.json", "AGENTS.md", ".harness/.gitignore"]);
+function isHarnessConfigFile(relativePath) {
+  return HARNESS_CONFIG_FILES.has(relativePath);
+}
+var PROJECT_MARKERS = [
+  "package.json",
+  "pom.xml",
+  "build.gradle",
+  "build.gradle.kts",
+  "pyproject.toml",
+  "setup.py",
+  "requirements.txt",
+  "Pipfile",
+  "go.mod",
+  "Cargo.toml",
+  "Makefile",
+  "CMakeLists.txt",
+  "meson.build"
+];
 function scoreDetectPatterns(targetDir, patterns) {
   let score = 0;
   for (const pattern of patterns) {
@@ -244,6 +270,9 @@ var TemplateEngine = class {
       for (const file of files.files) {
         const targetPath = path.join(targetDir, file.relativePath);
         const dir = path.dirname(targetPath);
+        if (!options.overwrite && options.existingProject && !isHarnessConfigFile(file.relativePath)) {
+          continue;
+        }
         if (!options.overwrite && isNonJsLanguage && NON_JSON_PACKAGE_CONFIGS.has(file.relativePath) && fs.existsSync(targetPath)) {
           skippedConfigs.push(file.relativePath);
           continue;
@@ -262,6 +291,13 @@ var TemplateEngine = class {
       );
     }
   }
+  /**
+   * Check whether the target directory already contains a project by looking for
+   * common build/package configuration files. Returns true if any marker is found.
+   */
+  isExistingProject(targetDir) {
+    return PROJECT_MARKERS.some((marker) => fs.existsSync(path.join(targetDir, marker)));
+  }
   detectFramework(targetDir) {
     try {
       const templatesResult = this.listTemplates();

package/dist/{chunk-RKZW3FDF.js → chunk-KVJZQ2MV.js}

@@ -1,6 +1,6 @@
 import {
   init_dist
-} from "./chunk-42ZZLMYD.js";
+} from "./chunk-ZIYLIYN4.js";
 import {
   Err,
   Ok

package/dist/{chunk-WEOGCL7B.js → chunk-LTCEV7VF.js}

@@ -1,6 +1,6 @@
 import {
   resolveProjectConfig
-} from "./chunk-XMEEYMGE.js";
+} from "./chunk-IQO7IINR.js";
 import {
   sanitizePath
 } from "./chunk-W6Y7ZW3Y.js";
@@ -49,7 +49,7 @@ async function handleValidateProject(input) {
   checks.config = "pass";
   const config = configResult.value;
   try {
-    const core = await import("./dist-T3DGV5UN.js");
+    const core = await import("./dist-ZV6GO6FA.js");
     if (typeof core.validateFileStructure === "function" && Array.isArray(config.conventions)) {
       const conventions = config.conventions;
       const structureResult = await core.validateFileStructure(projectPath, conventions);
@@ -68,7 +68,7 @@ async function handleValidateProject(input) {
   } catch {
   }
   try {
-    const core = await import("./dist-T3DGV5UN.js");
+    const core = await import("./dist-ZV6GO6FA.js");
     if (typeof core.validateAgentsMap === "function") {
       const agentsMapPath = path.join(projectPath, "AGENTS.md");
       const agentsResult = await core.validateAgentsMap(agentsMapPath);

package/dist/{chunk-Y5JA4J2M.js → chunk-LXPRO2FH.js}

@@ -1,9 +1,9 @@
 import {
   resolveConfig
-} from "./chunk-JUXFYB2K.js";
+} from "./chunk-TQRCODRJ.js";
 import {
   init_dist
-} from "./chunk-42ZZLMYD.js";
+} from "./chunk-ZIYLIYN4.js";
 import {
   Ok
 } from "./chunk-RL4VMEXL.js";

package/dist/{chunk-U2OMWI7Z.js → chunk-MCDCZMKN.js}

@@ -4,7 +4,7 @@ import {
 import {
   listPersonas,
   loadPersona
-} from "./chunk-VELT5VAG.js";
+} from "./chunk-FRDS4XGD.js";
 import {
   GENERATED_HEADER_AGENT,
   VALID_PLATFORMS,

package/dist/{chunk-4YEBV2FT.js → chunk-MLOGYWLY.js}

@@ -27,7 +27,7 @@ var runSecurityScanDefinition = {
 };
 async function handleRunSecurityScan(input) {
   try {
-    const core = await import("./dist-T3DGV5UN.js");
+    const core = await import("./dist-ZV6GO6FA.js");
     const projectRoot = sanitizePath(input.path);
     let configData = {};
     try {
@@ -114,7 +114,7 @@ var getSecurityTrendsDefinition = {
 };
 async function handleGetSecurityTrends(input) {
   try {
-    const core = await import("./dist-T3DGV5UN.js");
+    const core = await import("./dist-ZV6GO6FA.js");
     const projectRoot = sanitizePath(input.path);
     const manager = new core.SecurityTimelineManager(projectRoot);
     const trendOptions = {};

package/dist/{chunk-RDQGCHKD.js → chunk-NKQEMWGT.js}

@@ -1334,7 +1334,17 @@ var init_dist = __esm({
       typescript: /(?:export\s+)?(?:const|let|var)\s+(\w+)/,
       javascript: /(?:export\s+)?(?:const|let|var)\s+(\w+)/
     };
-    SUPPORTED_EXTENSIONS = /* @__PURE__ */ new Set([".ts", ".tsx", ".js", ".jsx", ".py", ".go", ".rs", ".java"]);
+    SUPPORTED_EXTENSIONS = /* @__PURE__ */ new Set([
+      ".ts",
+      ".tsx",
+      ".js",
+      ".jsx",
+      ".py",
+      ".go",
+      ".rs",
+      ".java",
+      ".groovy"
+    ]);
     SKIP_EXTENSIONS = /* @__PURE__ */ new Set([".d.ts"]);
     CodeIngestor = class {
       constructor(store) {
@@ -1348,23 +1358,34 @@ var init_dist = __esm({
         let edgesAdded = 0;
         const files = await this.findSourceFiles(rootDir);
         const nameToFiles = /* @__PURE__ */ new Map();
-        const fileContents = /* @__PURE__ */ new Map();
         for (const filePath of files) {
           try {
-            const result = await this.processFile(filePath, rootDir, nameToFiles, fileContents);
+            const result = await this.processFile(filePath, rootDir, nameToFiles);
             nodesAdded += result.nodesAdded;
             edgesAdded += result.edgesAdded;
           } catch (err) {
             errors.push(`${filePath}: ${err instanceof Error ? err.message : String(err)}`);
           }
         }
-        const callsEdges = this.extractCallsEdges(nameToFiles, fileContents);
-        for (const edge of callsEdges) {
-          this.store.addEdge(edge);
-          edgesAdded++;
+        for (const filePath of files) {
+          try {
+            const relativePath = path.relative(rootDir, filePath).replace(/\\/g, "/");
+            const content = await fs.readFile(filePath, "utf-8");
+            const callsEdges = this.extractCallsEdgesForFile(relativePath, content, nameToFiles);
+            for (const edge of callsEdges) {
+              this.store.addEdge(edge);
+              edgesAdded++;
+            }
+          } catch {
+          }
+        }
+        for (const filePath of files) {
+          try {
+            const content = await fs.readFile(filePath, "utf-8");
+            edgesAdded += this.extractReqAnnotationsForFile(filePath, content, rootDir);
+          } catch {
+          }
         }
-        edgesAdded += this.extractReqAnnotations(fileContents, rootDir);
-        fileContents.clear();
         return {
           nodesAdded,
           nodesUpdated: 0,
@@ -1374,14 +1395,13 @@ var init_dist = __esm({
           durationMs: Date.now() - start
         };
       }
-      async processFile(filePath, rootDir, nameToFiles, fileContents) {
+      async processFile(filePath, rootDir, nameToFiles) {
         let nodesAdded = 0;
         let edgesAdded = 0;
         const relativePath = path.relative(rootDir, filePath).replace(/\\/g, "/");
         const content = await fs.readFile(filePath, "utf-8");
         const stat2 = await fs.stat(filePath);
         const fileId = `file:${relativePath}`;
-        fileContents.set(relativePath, content);
         const fileNode = {
           id: fileId,
           type: "file",
@@ -1421,7 +1441,7 @@ var init_dist = __esm({
         const entries = await fs.readdir(dir, { withFileTypes: true });
         for (const entry of entries) {
           const fullPath = path.join(dir, entry.name);
-          if (entry.isDirectory() && entry.name !== "node_modules" && entry.name !== "dist") {
+          if (entry.isDirectory() && entry.name !== "node_modules" && entry.name !== "dist" && entry.name !== "target" && entry.name !== "build" && entry.name !== ".git" && entry.name !== "__pycache__" && entry.name !== ".venv" && entry.name !== ".turbo" && entry.name !== ".harness" && entry.name !== ".next" && entry.name !== ".vscode" && entry.name !== ".idea" && entry.name !== "vendor" && entry.name !== "out" && entry.name !== ".gradle" && entry.name !== ".gradle-home" && entry.name !== "bin" && entry.name !== "obj" && entry.name !== "venv" && entry.name !== "_build" && entry.name !== "deps" && entry.name !== "coverage" && entry.name !== ".nyc_output") {
             results.push(...await this.findSourceFiles(fullPath));
           } else if (entry.isFile() && isSupportedSourceFile(entry.name)) {
             results.push(fullPath);
@@ -1700,33 +1720,31 @@ var init_dist = __esm({
         return false;
       }
       /**
-       * Second pass: scan each file for identifiers matching known callable names,
+       * Scan a file for identifiers matching known callable names,
        * then create file-to-file "calls" edges. Uses regex heuristic (not AST).
        */
-      extractCallsEdges(nameToFiles, fileContents) {
+      extractCallsEdgesForFile(relativePath, content, nameToFiles) {
         const edges = [];
         const seen = /* @__PURE__ */ new Set();
-        for (const [filePath, content] of fileContents) {
-          const callerFileId = `file:${filePath}`;
-          const callPattern = /\b([a-zA-Z_$][\w$]*)\s*\(/g;
-          let match;
-          while ((match = callPattern.exec(content)) !== null) {
-            const name = match[1];
-            const targetFiles = nameToFiles.get(name);
-            if (!targetFiles) continue;
-            for (const targetFile of targetFiles) {
-              if (targetFile === filePath) continue;
-              const targetFileId = `file:${targetFile}`;
-              const key = `${callerFileId}|${targetFileId}`;
-              if (seen.has(key)) continue;
-              seen.add(key);
-              edges.push({
-                from: callerFileId,
-                to: targetFileId,
-                type: "calls",
-                metadata: { confidence: "regex" }
-              });
-            }
+        const callerFileId = `file:${relativePath}`;
+        const callPattern = /\b([a-zA-Z_$][\w$]*)\s*\(/g;
+        let match;
+        while ((match = callPattern.exec(content)) !== null) {
+          const name = match[1];
+          const targetFiles = nameToFiles.get(name);
+          if (!targetFiles) continue;
+          for (const targetFile of targetFiles) {
+            if (targetFile === relativePath) continue;
+            const targetFileId = `file:${targetFile}`;
+            const key = `${callerFileId}|${targetFileId}`;
+            if (seen.has(key)) continue;
+            seen.add(key);
+            edges.push({
+              from: callerFileId,
+              to: targetFileId,
+              type: "calls",
+              metadata: { confidence: "regex" }
+            });
           }
         }
         return edges;
@@ -1871,6 +1889,7 @@ var init_dist = __esm({
         if (/\.go$/.test(filePath)) return "go";
         if (/\.rs$/.test(filePath)) return "rust";
         if (/\.java$/.test(filePath)) return "java";
+        if (/\.groovy$/.test(filePath)) return "java";
         return "unknown";
       }
       /**
@@ -1878,40 +1897,38 @@ var init_dist = __esm({
        * linking requirement nodes to the annotated files.
        * Format: // @req <feature-name>#<index>
        */
-      extractReqAnnotations(fileContents, rootDir) {
+      extractReqAnnotationsForFile(filePath, content, rootDir) {
         const REQ_TAG = /(?:\/\/|#|\/\*)\s*@req\s+([\w-]+)#(\d+)/g;
         const reqNodes = this.store.findNodes({ type: "requirement" });
         let edgesAdded = 0;
-        for (const [filePath, content] of fileContents) {
-          let match;
-          REQ_TAG.lastIndex = 0;
-          while ((match = REQ_TAG.exec(content)) !== null) {
-            const featureName = match[1];
-            const reqIndex = parseInt(match[2], 10);
-            const reqNode = reqNodes.find(
-              (n) => n.metadata.featureName === featureName && n.metadata.index === reqIndex
+        let match;
+        REQ_TAG.lastIndex = 0;
+        while ((match = REQ_TAG.exec(content)) !== null) {
+          const featureName = match[1];
+          const reqIndex = parseInt(match[2], 10);
+          const reqNode = reqNodes.find(
+            (n) => n.metadata.featureName === featureName && n.metadata.index === reqIndex
+          );
+          if (!reqNode) {
+            console.warn(
+              `@req annotation references non-existent requirement: ${featureName}#${reqIndex} in ${filePath}`
             );
-            if (!reqNode) {
-              console.warn(
-                `@req annotation references non-existent requirement: ${featureName}#${reqIndex} in ${filePath}`
-              );
-              continue;
-            }
-            const relPath = path.relative(rootDir, filePath).replace(/\\/g, "/");
-            const fileNodeId = `file:${relPath}`;
-            this.store.addEdge({
-              from: reqNode.id,
-              to: fileNodeId,
-              type: "verified_by",
-              confidence: 1,
-              metadata: {
-                method: "annotation",
-                tag: `@req ${featureName}#${reqIndex}`,
-                confidence: 1
-              }
-            });
-            edgesAdded++;
+            continue;
           }
+          const relPath = path.relative(rootDir, filePath).replace(/\\/g, "/");
+          const fileNodeId = `file:${relPath}`;
+          this.store.addEdge({
+            from: reqNode.id,
+            to: fileNodeId,
+            type: "verified_by",
+            confidence: 1,
+            metadata: {
+              method: "annotation",
+              tag: `@req ${featureName}#${reqIndex}`,
+              confidence: 1
+            }
+          });
+          edgesAdded++;
         }
         return edgesAdded;
       }
@@ -2272,7 +2289,7 @@ var init_dist = __esm({
         const entries = await fs2.readdir(dir, { withFileTypes: true });
         for (const entry of entries) {
           const fullPath = path3.join(dir, entry.name);
-          if (entry.isDirectory()) {
+          if (entry.isDirectory() && entry.name !== "node_modules" && entry.name !== "dist" && entry.name !== "target" && entry.name !== "build" && entry.name !== ".git" && entry.name !== ".gradle" && entry.name !== ".harness" && entry.name !== "vendor" && entry.name !== "bin" && entry.name !== "obj" && entry.name !== "venv" && entry.name !== "_build" && entry.name !== "deps" && entry.name !== "coverage") {
             results.push(...await this.findMarkdownFiles(fullPath));
           } else if (entry.isFile() && entry.name.endsWith(".md")) {
             results.push(fullPath);
@@ -2411,7 +2428,7 @@ var init_dist = __esm({
         const entries = await fs3.readdir(dir, { withFileTypes: true });
         for (const entry of entries) {
           const fullPath = path4.join(dir, entry.name);
-          if (entry.isDirectory()) {
+          if (entry.isDirectory() && entry.name !== "node_modules" && entry.name !== "dist" && entry.name !== "target" && entry.name !== "build" && entry.name !== ".git" && entry.name !== ".gradle" && entry.name !== ".harness" && entry.name !== "vendor" && entry.name !== "bin" && entry.name !== "obj" && entry.name !== "venv" && entry.name !== "_build" && entry.name !== "deps" && entry.name !== "coverage") {
             results.push(...await this.findMarkdownFiles(fullPath));
           } else if (entry.isFile() && entry.name.endsWith(".md")) {
             results.push(fullPath);

package/dist/{chunk-X2JJ3CPG.js → chunk-PCOU2UXU.js}

@@ -7,10 +7,10 @@ import {
 import {
   findConfigFile,
   loadConfig
-} from "./chunk-JUXFYB2K.js";
+} from "./chunk-TQRCODRJ.js";
 import {
   init_dist
-} from "./chunk-42ZZLMYD.js";
+} from "./chunk-ZIYLIYN4.js";
 import {
   Ok
 } from "./chunk-RL4VMEXL.js";
@@ -35,7 +35,7 @@ var checkPerformanceDefinition = {
 };
 async function handleCheckPerformance(input) {
   try {
-    const { EntropyAnalyzer } = await import("./dist-T3DGV5UN.js");
+    const { EntropyAnalyzer } = await import("./dist-ZV6GO6FA.js");
     const typeFilter = input.type ?? "all";
     const projectPath = sanitizePath(input.path);
     let entryPoints;
@@ -58,10 +58,10 @@ async function handleCheckPerformance(input) {
     });
     let graphOptions;
     try {
-      const { loadGraphStore } = await import("./graph-loader-QMKXT454.js");
+      const { loadGraphStore } = await import("./graph-loader-KXVS3YK3.js");
       const store = await loadGraphStore(projectPath);
       if (store) {
-        const { GraphComplexityAdapter, GraphCouplingAdapter } = await import("./dist-GRW3X2ZQ.js");
+        const { GraphComplexityAdapter, GraphCouplingAdapter } = await import("./dist-HPWNWCT6.js");
         const complexityAdapter = new GraphComplexityAdapter(store);
         const couplingAdapter = new GraphCouplingAdapter(store);
         graphOptions = {
@@ -98,7 +98,7 @@ var getPerfBaselinesDefinition = {
 };
 async function handleGetPerfBaselines(input) {
   try {
-    const { BaselineManager } = await import("./dist-T3DGV5UN.js");
+    const { BaselineManager } = await import("./dist-ZV6GO6FA.js");
     const manager = new BaselineManager(sanitizePath(input.path));
     const baselines = manager.load();
     return resultToMcpResponse(
@@ -146,7 +146,7 @@ var updatePerfBaselinesDefinition = {
 };
 async function handleUpdatePerfBaselines(input) {
   try {
-    const { BaselineManager } = await import("./dist-T3DGV5UN.js");
+    const { BaselineManager } = await import("./dist-ZV6GO6FA.js");
     const manager = new BaselineManager(sanitizePath(input.path));
     manager.save(input.results, input.commitHash);
     const updated = manager.load();
@@ -176,7 +176,7 @@ var getCriticalPathsDefinition = {
 };
 async function handleGetCriticalPaths(input) {
   try {
-    const { CriticalPathResolver } = await import("./dist-T3DGV5UN.js");
+    const { CriticalPathResolver } = await import("./dist-ZV6GO6FA.js");
     const resolver = new CriticalPathResolver(sanitizePath(input.path));
     const result = await resolver.resolve();
     return resultToMcpResponse(Ok(result));