lean-spec 0.2.7-dev.20251127055844 → 0.2.7-dev.20251127073145

package/dist/{chunk-FTKNRIOE.js → chunk-2DAPKDV5.js}

@@ -6,7 +6,7 @@ import { fileURLToPath } from 'url';
 import * as path17 from 'path';
 import { dirname, join, resolve } from 'path';
 import { z } from 'zod';
-import * as fs11 from 'fs/promises';
+import * as fs12 from 'fs/promises';
 import { readFile, writeFile } from 'fs/promises';
 import chalk20 from 'chalk';
 import { Command } from 'commander';
@@ -43,7 +43,7 @@ var DEFAULT_CONFIG = {
 async function loadConfig(cwd = process.cwd()) {
   const configPath = path17.join(cwd, ".lean-spec", "config.json");
   try {
-    const content = await fs11.readFile(configPath, "utf-8");
+    const content = await fs12.readFile(configPath, "utf-8");
     const userConfig = JSON.parse(content);
     const merged = { ...DEFAULT_CONFIG, ...userConfig };
     normalizeLegacyPattern(merged);
@@ -55,8 +55,8 @@ async function loadConfig(cwd = process.cwd()) {
 async function saveConfig(config, cwd = process.cwd()) {
   const configDir = path17.join(cwd, ".lean-spec");
   const configPath = path17.join(configDir, "config.json");
-  await fs11.mkdir(configDir, { recursive: true });
-  await fs11.writeFile(configPath, JSON.stringify(config, null, 2), "utf-8");
+  await fs12.mkdir(configDir, { recursive: true });
+  await fs12.writeFile(configPath, JSON.stringify(config, null, 2), "utf-8");
 }
 function getToday(format = "YYYYMMDD") {
   const now = /* @__PURE__ */ new Date();
@@ -136,12 +136,12 @@ function extractGroup(extractor, dateFormat = "YYYYMMDD", fields, fallback) {
 async function loadSubFiles(specDir, options = {}) {
   const subFiles = [];
   try {
-    const entries = await fs11.readdir(specDir, { withFileTypes: true });
+    const entries = await fs12.readdir(specDir, { withFileTypes: true });
     for (const entry of entries) {
       if (entry.name === "README.md") continue;
       if (entry.isDirectory()) continue;
       const filePath = path17.join(specDir, entry.name);
-      const stat6 = await fs11.stat(filePath);
+      const stat6 = await fs12.stat(filePath);
       const ext = path17.extname(entry.name).toLowerCase();
       const isDocument = ext === ".md";
       const subFile = {
@@ -151,7 +151,7 @@ async function loadSubFiles(specDir, options = {}) {
         type: isDocument ? "document" : "asset"
       };
       if (isDocument && options.includeContent) {
-        subFile.content = await fs11.readFile(filePath, "utf-8");
+        subFile.content = await fs12.readFile(filePath, "utf-8");
       }
       subFiles.push(subFile);
     }
@@ -171,14 +171,14 @@ async function loadAllSpecs(options = {}) {
   const specsDir = path17.join(cwd, config.specsDir);
   const specs = [];
   try {
-    await fs11.access(specsDir);
+    await fs12.access(specsDir);
   } catch {
     return [];
   }
   const specPattern = /^(\d{2,})-/;
   async function loadSpecsFromDir(dir, relativePath = "") {
     try {
-      const entries = await fs11.readdir(dir, { withFileTypes: true });
+      const entries = await fs12.readdir(dir, { withFileTypes: true });
       for (const entry of entries) {
         if (!entry.isDirectory()) continue;
         if (entry.name === "archived" && relativePath === "") continue;
@@ -212,7 +212,7 @@ async function loadAllSpecs(options = {}) {
                 frontmatter
               };
               if (options.includeContent) {
-                specInfo.content = await fs11.readFile(specFile, "utf-8");
+                specInfo.content = await fs12.readFile(specFile, "utf-8");
               }
               if (options.includeSubFiles) {
                 specInfo.subFiles = await loadSubFiles(entryPath, {
@@ -287,7 +287,7 @@ async function getSpec(specPath) {
     fullPath = path17.join(specsDir, specPath);
   }
   try {
-    await fs11.access(fullPath);
+    await fs12.access(fullPath);
   } catch {
     return null;
   }
@@ -295,7 +295,7 @@ async function getSpec(specPath) {
   if (!specFile) return null;
   const frontmatter = await parseFrontmatter(specFile, config);
   if (!frontmatter) return null;
-  const content = await fs11.readFile(specFile, "utf-8");
+  const content = await fs12.readFile(specFile, "utf-8");
   const relativePath = path17.relative(specsDir, fullPath);
   const parts = relativePath.split(path17.sep);
   const date = parts[0] === "archived" ? parts[1] : parts[0];
@@ -319,7 +319,7 @@ async function getGlobalNextSeq(specsDir, digits) {
     const specPattern = createSpecDirPattern();
     async function scanDirectory(dir) {
       try {
-        const entries = await fs11.readdir(dir, { withFileTypes: true });
+        const entries = await fs12.readdir(dir, { withFileTypes: true });
         for (const entry of entries) {
           if (!entry.isDirectory()) continue;
           const match = entry.name.match(specPattern);
@@ -349,7 +349,7 @@ async function getGlobalNextSeq(specsDir, digits) {
 async function resolveSpecPath(specPath, cwd, specsDir) {
   if (path17.isAbsolute(specPath)) {
     try {
-      await fs11.access(specPath);
+      await fs12.access(specPath);
       return specPath;
     } catch {
       return null;
@@ -357,13 +357,13 @@ async function resolveSpecPath(specPath, cwd, specsDir) {
   }
   const cwdPath = path17.resolve(cwd, specPath);
   try {
-    await fs11.access(cwdPath);
+    await fs12.access(cwdPath);
     return cwdPath;
   } catch {
   }
   const specsPath = path17.join(specsDir, specPath);
   try {
-    await fs11.access(specsPath);
+    await fs12.access(specsPath);
     return specsPath;
   } catch {
   }
@@ -381,7 +381,7 @@ async function searchBySequence(specsDir, seqNum) {
   const specPattern = createSpecDirPattern();
   async function scanDirectory(dir) {
     try {
-      const entries = await fs11.readdir(dir, { withFileTypes: true });
+      const entries = await fs12.readdir(dir, { withFileTypes: true });
       for (const entry of entries) {
         if (!entry.isDirectory()) continue;
         const match = entry.name.match(specPattern);
@@ -404,7 +404,7 @@ async function searchBySequence(specsDir, seqNum) {
 async function searchInAllDirectories(specsDir, specName) {
   async function scanDirectory(dir) {
     try {
-      const entries = await fs11.readdir(dir, { withFileTypes: true });
+      const entries = await fs12.readdir(dir, { withFileTypes: true });
       for (const entry of entries) {
         if (!entry.isDirectory()) continue;
         if (entry.name === specName) {
@@ -754,11 +754,11 @@ async function loadSpecContent(specPath) {
   const specDir = spec.fullPath;
   let content = "";
   try {
-    const files = await fs11.readdir(specDir);
+    const files = await fs12.readdir(specDir);
     const mdFiles = files.filter((f) => f.endsWith(".md"));
     for (const file of mdFiles) {
       const filePath = path17.join(specDir, file);
-      const fileContent = await fs11.readFile(filePath, "utf-8");
+      const fileContent = await fs12.readFile(filePath, "utf-8");
       content += `
 
 ### ${file}
@@ -766,14 +766,14 @@ async function loadSpecContent(specPath) {
 ${fileContent}`;
     }
   } catch {
-    content = await fs11.readFile(spec.filePath, "utf-8");
+    content = await fs12.readFile(spec.filePath, "utf-8");
   }
   return content;
 }
 async function createWorktree(specPath, specName, cwd) {
   const worktreePath = path17.join(cwd, ".worktrees", `spec-${specName}`);
   const branchName = `feature/${specName}`;
-  await fs11.mkdir(path17.join(cwd, ".worktrees"), { recursive: true });
+  await fs12.mkdir(path17.join(cwd, ".worktrees"), { recursive: true });
   return new Promise((resolve3, reject) => {
     const child = spawn("git", ["worktree", "add", worktreePath, "-b", branchName], {
       cwd,
@@ -1452,7 +1452,7 @@ var TokenCounter = class {
    * Count tokens in a single file
    */
   async countFile(filePath, options = {}) {
-    const content = await fs11.readFile(filePath, "utf-8");
+    const content = await fs12.readFile(filePath, "utf-8");
     const tokens = await this.countString(content);
     const lines = content.split("\n").length;
     const result = {
@@ -1472,11 +1472,11 @@ var TokenCounter = class {
    * Count tokens in a spec (including sub-specs if requested)
    */
   async countSpec(specPath, options = {}) {
-    const stats = await fs11.stat(specPath);
+    const stats = await fs12.stat(specPath);
     if (stats.isFile()) {
       return this.countFile(specPath, options);
     }
-    const files = await fs11.readdir(specPath);
+    const files = await fs12.readdir(specPath);
     const mdFiles = files.filter((f) => f.endsWith(".md"));
     const filesToCount = [];
     if (mdFiles.includes("README.md")) {
@@ -1502,7 +1502,7 @@ var TokenCounter = class {
     }
     for (const file of filesToCount) {
       const filePath = path17.join(specPath, file);
-      const content = await fs11.readFile(filePath, "utf-8");
+      const content = await fs12.readFile(filePath, "utf-8");
       const tokens = await this.countString(content);
       const lines = content.split("\n").length;
       fileCounts.push({
@@ -1838,7 +1838,7 @@ var ComplexityValidator = class {
     let subSpecCount = 0;
     try {
       const specDir = path17.dirname(spec.filePath);
-      const files = await fs11.readdir(specDir);
+      const files = await fs12.readdir(specDir);
       const mdFiles = files.filter(
         (f) => f.endsWith(".md") && f !== "README.md"
       );
@@ -3266,7 +3266,7 @@ async function getGitInfo() {
 async function getProjectName(cwd = process.cwd()) {
   try {
     const packageJsonPath = path17.join(cwd, "package.json");
-    const content = await fs11.readFile(packageJsonPath, "utf-8");
+    const content = await fs12.readFile(packageJsonPath, "utf-8");
     const packageJson2 = JSON.parse(content);
     return packageJson2.name || null;
   } catch {
@@ -3505,7 +3505,7 @@ async function createSpec(name, options = {}) {
   const config = await loadConfig();
   const cwd = process.cwd();
   const specsDir = path17.join(cwd, config.specsDir);
-  await fs11.mkdir(specsDir, { recursive: true });
+  await fs12.mkdir(specsDir, { recursive: true });
   const seq = await getGlobalNextSeq(specsDir, config.structure.sequenceDigits);
   let specRelativePath;
   if (config.structure.pattern === "flat") {
@@ -3528,14 +3528,14 @@ async function createSpec(name, options = {}) {
   const specDir = path17.join(specsDir, specRelativePath);
   const specFile = path17.join(specDir, config.structure.defaultFile);
   try {
-    await fs11.access(specDir);
+    await fs12.access(specDir);
     throw new Error(`Spec already exists: ${sanitizeUserInput(specDir)}`);
   } catch (error) {
     if (error.code === "ENOENT") ; else {
       throw error;
     }
   }
-  await fs11.mkdir(specDir, { recursive: true });
+  await fs12.mkdir(specDir, { recursive: true });
   const templatesDir = path17.join(cwd, ".lean-spec", "templates");
   let templateName;
   if (options.template) {
@@ -3550,17 +3550,17 @@ async function createSpec(name, options = {}) {
   }
   let templatePath = path17.join(templatesDir, templateName);
   try {
-    await fs11.access(templatePath);
+    await fs12.access(templatePath);
   } catch {
     const legacyPath = path17.join(templatesDir, "spec-template.md");
     try {
-      await fs11.access(legacyPath);
+      await fs12.access(legacyPath);
       templatePath = legacyPath;
       templateName = "spec-template.md";
     } catch {
       const readmePath = path17.join(templatesDir, "README.md");
       try {
-        await fs11.access(readmePath);
+        await fs12.access(readmePath);
         templatePath = readmePath;
         templateName = "README.md";
       } catch {
@@ -3571,7 +3571,7 @@ async function createSpec(name, options = {}) {
   let content;
   let varContext;
   try {
-    const template = await fs11.readFile(templatePath, "utf-8");
+    const template = await fs12.readFile(templatePath, "utf-8");
     const date = (/* @__PURE__ */ new Date()).toISOString().split("T")[0];
     const title = options.title || name;
     varContext = await buildVariableContext(config, { name: title, date });
@@ -3615,9 +3615,9 @@ ${options.description}`
   } catch (error) {
     throw new Error(`Template not found: ${templatePath}. Run: lean-spec init`);
   }
-  await fs11.writeFile(specFile, content, "utf-8");
+  await fs12.writeFile(specFile, content, "utf-8");
   try {
-    const templateFiles = await fs11.readdir(templatesDir);
+    const templateFiles = await fs12.readdir(templatesDir);
     const additionalFiles = templateFiles.filter(
       (f) => f.endsWith(".md") && f !== templateName && f !== "spec-template.md" && f !== config.structure.defaultFile
     );
@@ -3625,9 +3625,9 @@ ${options.description}`
       for (const file of additionalFiles) {
         const srcPath = path17.join(templatesDir, file);
         const destPath = path17.join(specDir, file);
-        let fileContent = await fs11.readFile(srcPath, "utf-8");
+        let fileContent = await fs12.readFile(srcPath, "utf-8");
         fileContent = resolveVariables(fileContent, varContext);
-        await fs11.writeFile(destPath, fileContent, "utf-8");
+        await fs12.writeFile(destPath, fileContent, "utf-8");
       }
       console.log(chalk20.green(`\u2713 Created: ${sanitizeUserInput(specDir)}/`));
       console.log(chalk20.gray(`  Files: ${config.structure.defaultFile}, ${additionalFiles.join(", ")}`));
@@ -3672,10 +3672,10 @@ async function archiveSpec(specPath) {
     await updateFrontmatter(specFile, { status: "archived" });
   }
   const archiveDir = path17.join(specsDir, "archived");
-  await fs11.mkdir(archiveDir, { recursive: true });
+  await fs12.mkdir(archiveDir, { recursive: true });
   const specName = path17.basename(resolvedPath);
   const archivePath = path17.join(archiveDir, specName);
-  await fs11.rename(resolvedPath, archivePath);
+  await fs12.rename(resolvedPath, archivePath);
   console.log(chalk20.green(`\u2713 Archived: ${sanitizeUserInput(archivePath)}`));
 }
 
@@ -3727,7 +3727,7 @@ async function listSpecs(options = {}) {
   const cwd = process.cwd();
   const specsDir = path17.join(cwd, config.specsDir);
   try {
-    await fs11.access(specsDir);
+    await fs12.access(specsDir);
   } catch {
     console.log("");
     console.log("No specs directory found. Initialize with: lean-spec init");
@@ -4355,14 +4355,14 @@ async function listTemplates(cwd = process.cwd()) {
   console.log(chalk20.green("=== Project Templates ==="));
   console.log("");
   try {
-    await fs11.access(templatesDir);
+    await fs12.access(templatesDir);
   } catch {
     console.log(chalk20.yellow("No templates directory found."));
     console.log(chalk20.gray("Run: lean-spec init"));
     console.log("");
     return;
   }
-  const files = await fs11.readdir(templatesDir);
+  const files = await fs12.readdir(templatesDir);
   const templateFiles = files.filter((f) => f.endsWith(".md"));
   if (templateFiles.length === 0) {
     console.log(chalk20.yellow("No templates found."));
@@ -4381,7 +4381,7 @@ async function listTemplates(cwd = process.cwd()) {
   console.log(chalk20.cyan("Available files:"));
   for (const file of templateFiles) {
     const filePath = path17.join(templatesDir, file);
-    const stat6 = await fs11.stat(filePath);
+    const stat6 = await fs12.stat(filePath);
     const sizeKB = (stat6.size / 1024).toFixed(1);
     console.log(`  ${file} (${sizeKB} KB)`);
   }
@@ -4400,7 +4400,7 @@ async function showTemplate(templateName, cwd = process.cwd()) {
   const templateFile = config.templates[templateName];
   const templatePath = path17.join(templatesDir, templateFile);
   try {
-    const content = await fs11.readFile(templatePath, "utf-8");
+    const content = await fs12.readFile(templatePath, "utf-8");
     console.log("");
     console.log(chalk20.cyan(`=== Template: ${templateName} (${templateFile}) ===`));
     console.log("");
@@ -4417,7 +4417,7 @@ async function addTemplate(name, file, cwd = process.cwd()) {
   const templatesDir = path17.join(cwd, ".lean-spec", "templates");
   const templatePath = path17.join(templatesDir, file);
   try {
-    await fs11.access(templatePath);
+    await fs12.access(templatePath);
   } catch {
     console.error(chalk20.red(`Template file not found: ${file}`));
     console.error(chalk20.gray(`Expected at: ${templatePath}`));
@@ -4465,7 +4465,7 @@ async function copyTemplate(source, target, cwd = process.cwd()) {
   }
   const sourcePath = path17.join(templatesDir, sourceFile);
   try {
-    await fs11.access(sourcePath);
+    await fs12.access(sourcePath);
   } catch {
     console.error(chalk20.red(`Source template not found: ${source}`));
     console.error(chalk20.gray(`Expected at: ${sourcePath}`));
@@ -4473,7 +4473,7 @@ async function copyTemplate(source, target, cwd = process.cwd()) {
   }
   const targetFile = target.endsWith(".md") ? target : `${target}.md`;
   const targetPath = path17.join(templatesDir, targetFile);
-  await fs11.copyFile(sourcePath, targetPath);
+  await fs12.copyFile(sourcePath, targetPath);
   console.log(chalk20.green(`\u2713 Copied: ${sourceFile} \u2192 ${targetFile}`));
   if (!config.templates) {
     config.templates = {};
@@ -4619,7 +4619,7 @@ async function configDirExists(dirName) {
   const homeDir = process.env.HOME || process.env.USERPROFILE || "";
   if (!homeDir) return false;
   try {
-    await fs11.access(path17.join(homeDir, dirName));
+    await fs12.access(path17.join(homeDir, dirName));
     return true;
   } catch {
     return false;
@@ -4638,7 +4638,7 @@ async function extensionInstalled(extensionId) {
   ];
   for (const extDir of extensionDirs) {
     try {
-      const entries = await fs11.readdir(extDir);
+      const entries = await fs12.readdir(extDir);
       if (entries.some((e) => e.toLowerCase().startsWith(extensionId.toLowerCase()))) {
         return true;
       }
@@ -4721,7 +4721,7 @@ async function createAgentToolSymlinks(cwd, selectedTools) {
     const targetPath = path17.join(cwd, file);
     try {
       try {
-        await fs11.access(targetPath);
+        await fs12.access(targetPath);
         results.push({ file, skipped: true });
         continue;
       } catch {
@@ -4736,10 +4736,10 @@ async function createAgentToolSymlinks(cwd, selectedTools) {
 
 See AGENTS.md for the full LeanSpec AI agent instructions.
 `;
-        await fs11.writeFile(targetPath, windowsContent, "utf-8");
+        await fs12.writeFile(targetPath, windowsContent, "utf-8");
         results.push({ file, created: true, error: "created as copy (Windows)" });
       } else {
-        await fs11.symlink("AGENTS.md", targetPath);
+        await fs12.symlink("AGENTS.md", targetPath);
         results.push({ file, created: true });
       }
     } catch (error) {
@@ -4760,7 +4760,7 @@ async function detectExistingSystemPrompts(cwd) {
   const found = [];
   for (const file of commonFiles) {
     try {
-      await fs11.access(path17.join(cwd, file));
+      await fs12.access(path17.join(cwd, file));
       found.push(file);
     } catch {
     }
@@ -4772,13 +4772,13 @@ async function handleExistingFiles(action, existingFiles, templateDir, cwd, vari
     const filePath = path17.join(cwd, file);
     const templateFilePath = path17.join(templateDir, file);
     try {
-      await fs11.access(templateFilePath);
+      await fs12.access(templateFilePath);
     } catch {
       continue;
     }
     if (action === "merge-ai" && file === "AGENTS.md") {
-      const existing = await fs11.readFile(filePath, "utf-8");
-      let template = await fs11.readFile(templateFilePath, "utf-8");
+      const existing = await fs12.readFile(filePath, "utf-8");
+      let template = await fs12.readFile(templateFilePath, "utf-8");
       for (const [key, value] of Object.entries(variables)) {
         template = template.replace(new RegExp(`\\{${key}\\}`, "g"), value);
       }
@@ -4814,8 +4814,8 @@ Create a single consolidated AGENTS.md that:
 - Maintains clear structure and readability
 - Removes any duplicate or conflicting guidance
 `;
-      await fs11.mkdir(path17.dirname(promptPath), { recursive: true });
-      await fs11.writeFile(promptPath, aiPrompt, "utf-8");
+      await fs12.mkdir(path17.dirname(promptPath), { recursive: true });
+      await fs12.writeFile(promptPath, aiPrompt, "utf-8");
       console.log(chalk20.green(`\u2713 Created AI consolidation prompt`));
       console.log(chalk20.cyan(`  \u2192 ${promptPath}`));
       console.log("");
@@ -4826,8 +4826,8 @@ Create a single consolidated AGENTS.md that:
       console.log(chalk20.gray("  4. Review and commit the result"));
       console.log("");
     } else if (action === "merge-append" && file === "AGENTS.md") {
-      const existing = await fs11.readFile(filePath, "utf-8");
-      let template = await fs11.readFile(templateFilePath, "utf-8");
+      const existing = await fs12.readFile(filePath, "utf-8");
+      let template = await fs12.readFile(templateFilePath, "utf-8");
       for (const [key, value] of Object.entries(variables)) {
         template = template.replace(new RegExp(`\\{${key}\\}`, "g"), value);
       }
@@ -4838,26 +4838,26 @@ Create a single consolidated AGENTS.md that:
 ## LeanSpec Integration
 
 ${template.split("\n").slice(1).join("\n")}`;
-      await fs11.writeFile(filePath, merged, "utf-8");
+      await fs12.writeFile(filePath, merged, "utf-8");
       console.log(chalk20.green(`\u2713 Appended LeanSpec section to ${file}`));
       console.log(chalk20.yellow("  \u26A0 Note: May be verbose. Consider consolidating later."));
     } else if (action === "overwrite") {
       const backupPath = `${filePath}.backup`;
-      await fs11.rename(filePath, backupPath);
+      await fs12.rename(filePath, backupPath);
       console.log(chalk20.yellow(`\u2713 Backed up ${file} \u2192 ${file}.backup`));
-      let content = await fs11.readFile(templateFilePath, "utf-8");
+      let content = await fs12.readFile(templateFilePath, "utf-8");
       for (const [key, value] of Object.entries(variables)) {
         content = content.replace(new RegExp(`\\{${key}\\}`, "g"), value);
       }
-      await fs11.writeFile(filePath, content, "utf-8");
+      await fs12.writeFile(filePath, content, "utf-8");
       console.log(chalk20.green(`\u2713 Created new ${file}`));
       console.log(chalk20.gray(`  \u{1F4A1} Your original content is preserved in ${file}.backup`));
     }
   }
 }
 async function copyDirectory(src, dest, skipFiles = [], variables = {}) {
-  await fs11.mkdir(dest, { recursive: true });
-  const entries = await fs11.readdir(src, { withFileTypes: true });
+  await fs12.mkdir(dest, { recursive: true });
+  const entries = await fs12.readdir(src, { withFileTypes: true });
   for (const entry of entries) {
     const srcPath = path17.join(src, entry.name);
     const destPath = path17.join(dest, entry.name);
@@ -4868,13 +4868,13 @@ async function copyDirectory(src, dest, skipFiles = [], variables = {}) {
       await copyDirectory(srcPath, destPath, skipFiles, variables);
     } else {
       try {
-        await fs11.access(destPath);
+        await fs12.access(destPath);
       } catch {
-        let content = await fs11.readFile(srcPath, "utf-8");
+        let content = await fs12.readFile(srcPath, "utf-8");
         for (const [key, value] of Object.entries(variables)) {
           content = content.replace(new RegExp(`\\{${key}\\}`, "g"), value);
         }
-        await fs11.writeFile(destPath, content, "utf-8");
+        await fs12.writeFile(destPath, content, "utf-8");
       }
     }
   }
@@ -4882,7 +4882,7 @@ async function copyDirectory(src, dest, skipFiles = [], variables = {}) {
 async function getProjectName2(cwd) {
   try {
     const packageJsonPath = path17.join(cwd, "package.json");
-    const content = await fs11.readFile(packageJsonPath, "utf-8");
+    const content = await fs12.readFile(packageJsonPath, "utf-8");
     const pkg = JSON.parse(content);
     if (pkg.name) {
       return pkg.name;
@@ -5107,8 +5107,164 @@ async function attemptAutoMerge(cwd, promptPath, autoExecute) {
     return false;
   }
 }
+async function handleReinitialize(cwd, skipPrompts, forceReinit) {
+  const specsDir = path17.join(cwd, "specs");
+  let specCount = 0;
+  try {
+    const entries = await fs12.readdir(specsDir, { withFileTypes: true });
+    specCount = entries.filter((e) => e.isDirectory()).length;
+  } catch {
+  }
+  console.log("");
+  console.log(chalk20.yellow("\u26A0 LeanSpec is already initialized in this directory."));
+  if (specCount > 0) {
+    console.log(chalk20.cyan(`  Found ${specCount} spec${specCount > 1 ? "s" : ""} in specs/`));
+  }
+  console.log("");
+  if (forceReinit) {
+    console.log(chalk20.gray("Force flag detected. Resetting configuration..."));
+    return "reset-config";
+  }
+  if (skipPrompts) {
+    console.log(chalk20.gray("Using safe upgrade (preserving all existing files)"));
+    return "upgrade";
+  }
+  const strategy = await select({
+    message: "What would you like to do?",
+    choices: [
+      {
+        name: "Upgrade configuration (recommended)",
+        value: "upgrade",
+        description: "Update config to latest version. Keeps specs and AGENTS.md untouched."
+      },
+      {
+        name: "Reset configuration",
+        value: "reset-config",
+        description: "Fresh config from template. Keeps specs/ directory."
+      },
+      {
+        name: "Full reset",
+        value: "full-reset",
+        description: "Remove .lean-spec/, specs/, and AGENTS.md. Start completely fresh."
+      },
+      {
+        name: "Cancel",
+        value: "cancel",
+        description: "Exit without changes."
+      }
+    ]
+  });
+  if (strategy === "full-reset") {
+    const warnings = [];
+    if (specCount > 0) {
+      warnings.push(`${specCount} spec${specCount > 1 ? "s" : ""} in specs/`);
+    }
+    try {
+      await fs12.access(path17.join(cwd, "AGENTS.md"));
+      warnings.push("AGENTS.md");
+    } catch {
+    }
+    if (warnings.length > 0) {
+      console.log("");
+      console.log(chalk20.red("\u26A0 This will permanently delete:"));
+      for (const warning of warnings) {
+        console.log(chalk20.red(`  - ${warning}`));
+      }
+      console.log("");
+      const confirmed = await confirm({
+        message: "Are you sure you want to continue?",
+        default: false
+      });
+      if (!confirmed) {
+        console.log(chalk20.gray("Cancelled."));
+        return "cancel";
+      }
+    }
+    console.log(chalk20.gray("Performing full reset..."));
+    await fs12.rm(path17.join(cwd, ".lean-spec"), { recursive: true, force: true });
+    console.log(chalk20.gray("  Removed .lean-spec/"));
+    try {
+      await fs12.rm(specsDir, { recursive: true, force: true });
+      console.log(chalk20.gray("  Removed specs/"));
+    } catch {
+    }
+    for (const file of ["AGENTS.md", "CLAUDE.md", "GEMINI.md"]) {
+      try {
+        await fs12.rm(path17.join(cwd, file), { force: true });
+        console.log(chalk20.gray(`  Removed ${file}`));
+      } catch {
+      }
+    }
+  }
+  return strategy;
+}
+async function upgradeConfig(cwd) {
+  const configPath = path17.join(cwd, ".lean-spec", "config.json");
+  let existingConfig;
+  try {
+    const content = await fs12.readFile(configPath, "utf-8");
+    existingConfig = JSON.parse(content);
+  } catch {
+    console.error(chalk20.red("Error reading existing config"));
+    process.exit(1);
+  }
+  const templateConfigPath = path17.join(TEMPLATES_DIR, "standard", "config.json");
+  let templateConfig;
+  try {
+    const content = await fs12.readFile(templateConfigPath, "utf-8");
+    templateConfig = JSON.parse(content).config;
+  } catch {
+    console.error(chalk20.red("Error reading template config"));
+    process.exit(1);
+  }
+  const upgradedConfig = {
+    ...templateConfig,
+    ...existingConfig,
+    // Deep merge structure
+    structure: {
+      ...templateConfig.structure,
+      ...existingConfig.structure
+    }
+  };
+  const templatesDir = path17.join(cwd, ".lean-spec", "templates");
+  try {
+    await fs12.mkdir(templatesDir, { recursive: true });
+  } catch {
+  }
+  const templateFiles = ["spec-template.md"];
+  let templatesUpdated = false;
+  for (const file of templateFiles) {
+    const destPath = path17.join(templatesDir, file);
+    try {
+      await fs12.access(destPath);
+    } catch {
+      const srcPath = path17.join(TEMPLATES_DIR, "standard", "files", "README.md");
+      try {
+        await fs12.copyFile(srcPath, destPath);
+        templatesUpdated = true;
+        console.log(chalk20.green(`\u2713 Added missing template: ${file}`));
+      } catch {
+      }
+    }
+  }
+  await saveConfig(upgradedConfig, cwd);
+  console.log("");
+  console.log(chalk20.green("\u2713 Configuration upgraded!"));
+  console.log("");
+  console.log(chalk20.gray("What was updated:"));
+  console.log(chalk20.gray("  - Config merged with latest defaults"));
+  if (templatesUpdated) {
+    console.log(chalk20.gray("  - Missing templates added"));
+  }
+  console.log("");
+  console.log(chalk20.gray("What was preserved:"));
+  console.log(chalk20.gray("  - Your specs/ directory"));
+  console.log(chalk20.gray("  - Your AGENTS.md"));
+  console.log(chalk20.gray("  - Your custom settings"));
+  console.log("");
+}
 function initCommand() {
-  return new Command("init").description("Initialize LeanSpec in current directory").option("-y, --yes", "Skip prompts and use defaults (quick start with standard template)").option("--template <name>", "Use specific template (standard or detailed)").option("--example [name]", "Scaffold an example project for tutorials (interactive if no name provided)").option("--name <dirname>", "Custom directory name for example project").option("--list", "List available example projects").option("--agent-tools <tools>", 'AI tools to create symlinks for (comma-separated: claude,gemini,copilot or "all" or "none")').action(async (options) => {
+  return new Command("init").description("Initialize LeanSpec in current directory").option("-y, --yes", "Skip prompts and use defaults (quick start with standard template)").option("-f, --force", "Force re-initialization (resets config, keeps specs)").option("--template <name>", "Use specific template (standard or detailed)").option("--example [name]", "Scaffold an example project for tutorials (interactive if no name provided)").option("--name <dirname>", "Custom directory name for example project").option("--list", "List available example projects").option("--agent-tools <tools>", 'AI tools to create symlinks for (comma-separated: claude,gemini,copilot or "all" or "none")').action(async (options) => {
     if (options.list) {
       await listExamples();
       return;
@@ -5117,18 +5273,32 @@ function initCommand() {
       await scaffoldExample(options.example, options.name);
       return;
     }
-    await initProject(options.yes, options.template, options.agentTools);
+    await initProject(options.yes, options.template, options.agentTools, options.force);
   });
 }
-async function initProject(skipPrompts = false, templateOption, agentToolsOption) {
+async function initProject(skipPrompts = false, templateOption, agentToolsOption, forceReinit = false) {
   const cwd = process.cwd();
+  const configPath = path17.join(cwd, ".lean-spec", "config.json");
+  let isAlreadyInitialized = false;
   try {
-    await fs11.access(path17.join(cwd, ".lean-spec", "config.json"));
-    console.log(chalk20.yellow("\u26A0 LeanSpec already initialized in this directory."));
-    console.log(chalk20.gray("To reinitialize, delete .lean-spec/ directory first."));
-    return;
+    await fs12.access(configPath);
+    isAlreadyInitialized = true;
   } catch {
   }
+  if (isAlreadyInitialized) {
+    const strategy = await handleReinitialize(cwd, skipPrompts, forceReinit);
+    if (strategy === "cancel") {
+      return;
+    }
+    if (strategy === "upgrade") {
+      await upgradeConfig(cwd);
+      return;
+    }
+    if (strategy === "reset-config") {
+      await fs12.rm(path17.join(cwd, ".lean-spec"), { recursive: true, force: true });
+      console.log(chalk20.gray("Removed .lean-spec/ configuration"));
+    }
+  }
   console.log("");
   console.log(chalk20.green("Welcome to LeanSpec!"));
   console.log("");
@@ -5201,7 +5371,7 @@ async function initProject(skipPrompts = false, templateOption, agentToolsOption
   const templateConfigPath = path17.join(templateDir, "config.json");
   let templateConfig;
   try {
-    const content = await fs11.readFile(templateConfigPath, "utf-8");
+    const content = await fs12.readFile(templateConfigPath, "utf-8");
     templateConfig = JSON.parse(content).config;
   } catch {
     console.error(chalk20.red(`Error: Template not found: ${templateName}`));
@@ -5270,30 +5440,39 @@ async function initProject(skipPrompts = false, templateOption, agentToolsOption
       }
       console.log("");
     }
-    const toolChoices = Object.entries(AI_TOOL_CONFIGS).map(([key, config]) => ({
+    const symlinkTools = Object.entries(AI_TOOL_CONFIGS).filter(([, config]) => config.usesSymlink).map(([key, config]) => ({
       name: config.description,
       value: key,
       checked: detectedDefaults.includes(key)
     }));
-    selectedAgentTools = await checkbox({
-      message: "Which AI tools do you use? (creates symlinks for tool-specific instruction files)",
-      choices: toolChoices
-    });
+    if (symlinkTools.length > 0) {
+      console.log("");
+      console.log(chalk20.gray("AGENTS.md will be created as the primary instruction file."));
+      console.log(chalk20.gray("Some AI tools (Claude Code, Gemini CLI) use their own filenames."));
+      console.log("");
+      const symlinkSelection = await checkbox({
+        message: "Create symlinks for additional AI tools?",
+        choices: symlinkTools
+      });
+      selectedAgentTools = symlinkSelection;
+    } else {
+      selectedAgentTools = [];
+    }
   }
   const templatesDir = path17.join(cwd, ".lean-spec", "templates");
   try {
-    await fs11.mkdir(templatesDir, { recursive: true });
+    await fs12.mkdir(templatesDir, { recursive: true });
   } catch (error) {
     console.error(chalk20.red("Error creating templates directory:"), error);
     process.exit(1);
   }
   const templateFilesDir = path17.join(templateDir, "files");
   try {
-    const files = await fs11.readdir(templateFilesDir);
+    const files = await fs12.readdir(templateFilesDir);
     if (templateName === "standard") {
       const readmePath = path17.join(templateFilesDir, "README.md");
       const targetSpecPath = path17.join(templatesDir, "spec-template.md");
-      await fs11.copyFile(readmePath, targetSpecPath);
+      await fs12.copyFile(readmePath, targetSpecPath);
       console.log(chalk20.green("\u2713 Created .lean-spec/templates/spec-template.md"));
       templateConfig.template = "spec-template.md";
       templateConfig.templates = {
@@ -5303,7 +5482,7 @@ async function initProject(skipPrompts = false, templateOption, agentToolsOption
       for (const file of files) {
         const srcPath = path17.join(templateFilesDir, file);
         const destPath = path17.join(templatesDir, file);
-        await fs11.copyFile(srcPath, destPath);
+        await fs12.copyFile(srcPath, destPath);
       }
       console.log(chalk20.green(`\u2713 Created .lean-spec/templates/ with ${files.length} files`));
       console.log(chalk20.gray(`  Files: ${files.join(", ")}`));
@@ -5381,9 +5560,9 @@ async function initProject(skipPrompts = false, templateOption, agentToolsOption
     const agentsSourcePath = path17.join(templateDir, "AGENTS.md");
     const agentsTargetPath = path17.join(cwd, "AGENTS.md");
     try {
-      let agentsContent = await fs11.readFile(agentsSourcePath, "utf-8");
+      let agentsContent = await fs12.readFile(agentsSourcePath, "utf-8");
       agentsContent = agentsContent.replace(/\{project_name\}/g, projectName);
-      await fs11.writeFile(agentsTargetPath, agentsContent, "utf-8");
+      await fs12.writeFile(agentsTargetPath, agentsContent, "utf-8");
       console.log(chalk20.green("\u2713 Created AGENTS.md"));
     } catch (error) {
       console.error(chalk20.red("Error copying AGENTS.md:"), error);
@@ -5404,7 +5583,7 @@ async function initProject(skipPrompts = false, templateOption, agentToolsOption
   }
   const filesDir = path17.join(templateDir, "files");
   try {
-    const filesToCopy = await fs11.readdir(filesDir);
+    const filesToCopy = await fs12.readdir(filesDir);
     const hasOtherFiles = filesToCopy.some((f) => !f.match(/\.(md)$/i) || !["README.md", "DESIGN.md", "PLAN.md", "TEST.md"].includes(f));
     if (hasOtherFiles) {
       await copyDirectory(filesDir, cwd, [...skipFiles, "README.md", "DESIGN.md", "PLAN.md", "TEST.md"], { project_name: projectName });
@@ -5416,7 +5595,7 @@ async function initProject(skipPrompts = false, templateOption, agentToolsOption
   }
   const specsDir = path17.join(cwd, "specs");
   try {
-    await fs11.mkdir(specsDir, { recursive: true });
+    await fs12.mkdir(specsDir, { recursive: true });
     console.log(chalk20.green("\u2713 Created specs/ directory"));
   } catch (error) {
     console.error(chalk20.red("Error creating specs directory:"), error);
@@ -5425,9 +5604,10 @@ async function initProject(skipPrompts = false, templateOption, agentToolsOption
   console.log("");
   console.log(chalk20.green("\u2713 LeanSpec initialized!"));
   console.log("");
-  console.log("Next steps:");
-  console.log(chalk20.cyan("  1. Edit AGENTS.md") + chalk20.gray(' \u2192 Fill in the "\u{1F4CB} Project Context" section'));
-  console.log(chalk20.cyan("  2. Create your first spec:") + chalk20.gray(" lean-spec create my-feature"));
+  console.log(chalk20.cyan("You're ready to go!") + chalk20.gray(" Ask your AI to create a spec for your next feature."));
+  console.log("");
+  console.log(chalk20.gray('Example: "Create a spec for user authentication"'));
+  console.log(chalk20.gray("Learn more: https://lean-spec.dev/docs/guide/getting-started"));
   console.log("");
 }
 async function listExamples() {
@@ -5467,7 +5647,7 @@ async function scaffoldExample(exampleName, customName) {
   const targetDirName = customName || exampleName;
   const targetPath = path17.join(process.cwd(), targetDirName);
   try {
-    const files = await fs11.readdir(targetPath);
+    const files = await fs12.readdir(targetPath);
     const nonGitFiles = files.filter((f) => f !== ".git");
     if (nonGitFiles.length > 0) {
       console.error(chalk20.red(`Error: Directory "${targetDirName}" already exists and is not empty.`));
@@ -5480,7 +5660,7 @@ async function scaffoldExample(exampleName, customName) {
   console.log(chalk20.green(`Setting up example: ${example.title}`));
   console.log(chalk20.gray(example.description));
   console.log("");
-  await fs11.mkdir(targetPath, { recursive: true });
+  await fs12.mkdir(targetPath, { recursive: true });
   console.log(chalk20.green(`\u2713 Created directory: ${targetDirName}/`));
   const examplePath = path17.join(EXAMPLES_DIR, exampleName);
   await copyDirectoryRecursive(examplePath, targetPath);
@@ -5540,27 +5720,27 @@ async function selectExample() {
   return choice;
 }
 async function copyDirectoryRecursive(src, dest) {
-  const entries = await fs11.readdir(src, { withFileTypes: true });
+  const entries = await fs12.readdir(src, { withFileTypes: true });
   for (const entry of entries) {
     const srcPath = path17.join(src, entry.name);
     const destPath = path17.join(dest, entry.name);
     if (entry.isDirectory()) {
-      await fs11.mkdir(destPath, { recursive: true });
+      await fs12.mkdir(destPath, { recursive: true });
       await copyDirectoryRecursive(srcPath, destPath);
     } else {
-      await fs11.copyFile(srcPath, destPath);
+      await fs12.copyFile(srcPath, destPath);
     }
   }
 }
 async function detectPackageManager() {
   const cwd = process.cwd();
   try {
-    await fs11.access(path17.join(cwd, "..", "pnpm-lock.yaml"));
+    await fs12.access(path17.join(cwd, "..", "pnpm-lock.yaml"));
     return "pnpm";
   } catch {
   }
   try {
-    await fs11.access(path17.join(cwd, "..", "yarn.lock"));
+    await fs12.access(path17.join(cwd, "..", "yarn.lock"));
     return "yarn";
   } catch {
   }
@@ -5589,8 +5769,8 @@ async function showFiles(specPath, options = {}) {
   }
   const subFiles = await loadSubFiles(spec.fullPath);
   if (options.json) {
-    const readmeStat2 = await fs11.stat(spec.filePath);
-    const readmeContent2 = await fs11.readFile(spec.filePath, "utf-8");
+    const readmeStat2 = await fs12.stat(spec.filePath);
+    const readmeContent2 = await fs12.readFile(spec.filePath, "utf-8");
     const readmeTokens2 = await countTokens({ content: readmeContent2 });
     const jsonOutput = {
       spec: spec.name,
@@ -5617,9 +5797,9 @@ async function showFiles(specPath, options = {}) {
   console.log(chalk20.cyan(`\u{1F4C4} Files in ${sanitizeUserInput(spec.name)}`));
   console.log("");
   console.log(chalk20.green("Required:"));
-  const readmeStat = await fs11.stat(spec.filePath);
+  const readmeStat = await fs12.stat(spec.filePath);
   const readmeSize = formatSize(readmeStat.size);
-  const readmeContent = await fs11.readFile(spec.filePath, "utf-8");
+  const readmeContent = await fs12.readFile(spec.filePath, "utf-8");
   const readmeTokens = await countTokens({ content: readmeContent });
   console.log(chalk20.green(`  \u2713 README.md              (${readmeSize}, ~${readmeTokens.total.toLocaleString()} tokens)  Main spec`));
   console.log("");
@@ -5640,7 +5820,7 @@ async function showFiles(specPath, options = {}) {
     console.log(chalk20.cyan("Documents:"));
     for (const file of documents) {
       const size = formatSize(file.size);
-      const content = await fs11.readFile(file.path, "utf-8");
+      const content = await fs12.readFile(file.path, "utf-8");
       const tokenCount = await countTokens({ content });
       console.log(chalk20.cyan(`  \u2713 ${sanitizeUserInput(file.name).padEnd(20)} (${size}, ~${tokenCount.total.toLocaleString()} tokens)`));
     }
@@ -6709,7 +6889,7 @@ async function validateSpecs(options = {}) {
   for (const spec of specs) {
     let content;
     try {
-      content = await fs11.readFile(spec.filePath, "utf-8");
+      content = await fs12.readFile(spec.filePath, "utf-8");
     } catch (error) {
       console.error(chalk20.red(`Error reading ${spec.filePath}:`), error);
       continue;
@@ -6763,7 +6943,7 @@ function migrateCommand(inputPath, options = {}) {
 async function migrateSpecs(inputPath, options = {}) {
   const config = await loadConfig();
   try {
-    const stats = await fs11.stat(inputPath);
+    const stats = await fs12.stat(inputPath);
     if (!stats.isDirectory()) {
       console.error("\x1B[31m\u274C Error:\x1B[0m Input path must be a directory");
       process.exit(1);
@@ -6791,7 +6971,7 @@ async function migrateSpecs(inputPath, options = {}) {
 async function scanDocuments(dirPath) {
   const documents = [];
   async function scanRecursive(currentPath) {
-    const entries = await fs11.readdir(currentPath, { withFileTypes: true });
+    const entries = await fs12.readdir(currentPath, { withFileTypes: true });
     for (const entry of entries) {
       const fullPath = path17.join(currentPath, entry.name);
       if (entry.isDirectory()) {
@@ -6800,7 +6980,7 @@ async function scanDocuments(dirPath) {
         }
       } else if (entry.isFile()) {
         if (entry.name.endsWith(".md") || entry.name.endsWith(".markdown")) {
-          const stats = await fs11.stat(fullPath);
+          const stats = await fs12.stat(fullPath);
           documents.push({
             path: fullPath,
             name: entry.name,
@@ -9164,7 +9344,7 @@ async function readSpecContent(specPath, cwd = process.cwd()) {
     if (resolvedPath) {
       targetFile = path17.join(resolvedPath, filePart);
       try {
-        await fs11.access(targetFile);
+        await fs12.access(targetFile);
       } catch {
         return null;
       }
@@ -9183,7 +9363,7 @@ async function readSpecContent(specPath, cwd = process.cwd()) {
   if (!targetFile) {
     return null;
   }
-  const rawContent = await fs11.readFile(targetFile, "utf-8");
+  const rawContent = await fs12.readFile(targetFile, "utf-8");
   const fileName = path17.basename(targetFile);
   const isSubSpec = fileName !== config.structure.defaultFile;
   let frontmatter = null;
@@ -9348,7 +9528,7 @@ async function openSpec(specPath, options = {}) {
     if (resolvedPath) {
       targetFile = path17.join(resolvedPath, filePart);
       try {
-        await fs11.access(targetFile);
+        await fs12.access(targetFile);
       } catch {
         targetFile = null;
       }
@@ -11204,5 +11384,5 @@ if (import.meta.url === `file://${process.argv[1]}`) {
 }
 
 export { agentCommand, analyzeCommand, archiveCommand, backfillCommand, boardCommand, checkCommand, compactCommand, createCommand, createMcpServer, depsCommand, examplesCommand, filesCommand, ganttCommand, initCommand, linkCommand, listCommand, mcpCommand, migrateCommand, openCommand, searchCommand, splitCommand, statsCommand, templatesCommand, timelineCommand, tokensCommand, uiCommand, unlinkCommand, updateCommand, validateCommand, viewCommand };
-//# sourceMappingURL=chunk-FTKNRIOE.js.map
-//# sourceMappingURL=chunk-FTKNRIOE.js.map
+//# sourceMappingURL=chunk-2DAPKDV5.js.map
+//# sourceMappingURL=chunk-2DAPKDV5.js.map