@rely-ai/caliber 1.3.3 → 1.4.0

package/dist/bin.js

@@ -51,7 +51,7 @@ var init_constants = __esm({
 
 // src/cli.ts
 import { Command } from "commander";
-import fs26 from "fs";
+import fs27 from "fs";
 import path22 from "path";
 import { fileURLToPath } from "url";
 
@@ -61,7 +61,7 @@ import ora2 from "ora";
 import readline4 from "readline";
 import select2 from "@inquirer/select";
 import checkbox from "@inquirer/checkbox";
-import fs19 from "fs";
+import fs20 from "fs";
 
 // src/fingerprint/index.ts
 import fs6 from "fs";
@@ -2204,25 +2204,92 @@ function openDiffsInEditor(editor, files) {
 // src/commands/onboard.ts
 import { createTwoFilesPatch } from "diff";
 
-// src/lib/hooks.ts
+// src/commands/setup-files.ts
 import fs14 from "fs";
+function buildSkillContent(skill) {
+  const frontmatter = `---
+name: ${skill.name}
+description: ${skill.description}
+---
+
+`;
+  return frontmatter + skill.content;
+}
+function collectSetupFiles(setup) {
+  const files = [];
+  const claude = setup.claude;
+  const cursor = setup.cursor;
+  const codex = setup.codex;
+  if (claude) {
+    if (claude.claudeMd) files.push({ path: "CLAUDE.md", content: claude.claudeMd });
+    const skills = claude.skills;
+    if (Array.isArray(skills)) {
+      for (const skill of skills) {
+        files.push({ path: `.claude/skills/${skill.name}/SKILL.md`, content: buildSkillContent(skill) });
+      }
+    }
+  }
+  if (codex) {
+    if (codex.agentsMd) files.push({ path: "AGENTS.md", content: codex.agentsMd });
+    const codexSkills = codex.skills;
+    if (Array.isArray(codexSkills)) {
+      for (const skill of codexSkills) {
+        files.push({ path: `.agents/skills/${skill.name}/SKILL.md`, content: buildSkillContent(skill) });
+      }
+    }
+  }
+  if (cursor) {
+    if (cursor.cursorrules) files.push({ path: ".cursorrules", content: cursor.cursorrules });
+    const cursorSkills = cursor.skills;
+    if (Array.isArray(cursorSkills)) {
+      for (const skill of cursorSkills) {
+        files.push({ path: `.cursor/skills/${skill.name}/SKILL.md`, content: buildSkillContent(skill) });
+      }
+    }
+    const rules = cursor.rules;
+    if (Array.isArray(rules)) {
+      for (const rule of rules) {
+        files.push({ path: `.cursor/rules/${rule.filename}`, content: rule.content });
+      }
+    }
+  }
+  if (!fs14.existsSync("AGENTS.md") && !(codex && codex.agentsMd)) {
+    const agentRefs = [];
+    if (claude) agentRefs.push("See `CLAUDE.md` for Claude Code configuration.");
+    if (cursor) agentRefs.push("See `.cursor/rules/` for Cursor rules.");
+    if (agentRefs.length === 0) agentRefs.push("See CLAUDE.md and .cursor/rules/ for agent configurations.");
+    files.push({
+      path: "AGENTS.md",
+      content: `# AGENTS.md
+
+This project uses AI coding agents configured by [Caliber](https://github.com/rely-ai-org/caliber).
+
+${agentRefs.join(" ")}
+`
+    });
+  }
+  return files;
+}
+
+// src/lib/hooks.ts
+import fs15 from "fs";
 import path12 from "path";
 import { execSync as execSync5 } from "child_process";
 var SETTINGS_PATH = path12.join(".claude", "settings.json");
 var HOOK_COMMAND = "caliber refresh --quiet";
 var HOOK_DESCRIPTION = "Caliber: auto-refreshing docs based on code changes";
 function readSettings() {
-  if (!fs14.existsSync(SETTINGS_PATH)) return {};
+  if (!fs15.existsSync(SETTINGS_PATH)) return {};
   try {
-    return JSON.parse(fs14.readFileSync(SETTINGS_PATH, "utf-8"));
+    return JSON.parse(fs15.readFileSync(SETTINGS_PATH, "utf-8"));
   } catch {
     return {};
   }
 }
 function writeSettings(settings) {
   const dir = path12.dirname(SETTINGS_PATH);
-  if (!fs14.existsSync(dir)) fs14.mkdirSync(dir, { recursive: true });
-  fs14.writeFileSync(SETTINGS_PATH, JSON.stringify(settings, null, 2));
+  if (!fs15.existsSync(dir)) fs15.mkdirSync(dir, { recursive: true });
+  fs15.writeFileSync(SETTINGS_PATH, JSON.stringify(settings, null, 2));
 }
 function findHookIndex(sessionEnd) {
   return sessionEnd.findIndex(
@@ -2291,8 +2358,8 @@ function getPreCommitPath() {
 }
 function isPreCommitHookInstalled() {
   const hookPath = getPreCommitPath();
-  if (!hookPath || !fs14.existsSync(hookPath)) return false;
-  const content = fs14.readFileSync(hookPath, "utf-8");
+  if (!hookPath || !fs15.existsSync(hookPath)) return false;
+  const content = fs15.readFileSync(hookPath, "utf-8");
   return content.includes(PRECOMMIT_START);
 }
 function installPreCommitHook() {
@@ -2302,40 +2369,40 @@ function installPreCommitHook() {
   const hookPath = getPreCommitPath();
   if (!hookPath) return { installed: false, alreadyInstalled: false };
   const hooksDir = path12.dirname(hookPath);
-  if (!fs14.existsSync(hooksDir)) fs14.mkdirSync(hooksDir, { recursive: true });
+  if (!fs15.existsSync(hooksDir)) fs15.mkdirSync(hooksDir, { recursive: true });
   let content = "";
-  if (fs14.existsSync(hookPath)) {
-    content = fs14.readFileSync(hookPath, "utf-8");
+  if (fs15.existsSync(hookPath)) {
+    content = fs15.readFileSync(hookPath, "utf-8");
     if (!content.endsWith("\n")) content += "\n";
     content += "\n" + PRECOMMIT_BLOCK + "\n";
   } else {
     content = "#!/bin/sh\n\n" + PRECOMMIT_BLOCK + "\n";
   }
-  fs14.writeFileSync(hookPath, content);
-  fs14.chmodSync(hookPath, 493);
+  fs15.writeFileSync(hookPath, content);
+  fs15.chmodSync(hookPath, 493);
   return { installed: true, alreadyInstalled: false };
 }
 function removePreCommitHook() {
   const hookPath = getPreCommitPath();
-  if (!hookPath || !fs14.existsSync(hookPath)) {
+  if (!hookPath || !fs15.existsSync(hookPath)) {
     return { removed: false, notFound: true };
   }
-  let content = fs14.readFileSync(hookPath, "utf-8");
+  let content = fs15.readFileSync(hookPath, "utf-8");
   if (!content.includes(PRECOMMIT_START)) {
     return { removed: false, notFound: true };
   }
   const regex = new RegExp(`\\n?${PRECOMMIT_START}[\\s\\S]*?${PRECOMMIT_END}\\n?`);
   content = content.replace(regex, "\n");
   if (content.trim() === "#!/bin/sh" || content.trim() === "") {
-    fs14.unlinkSync(hookPath);
+    fs15.unlinkSync(hookPath);
   } else {
-    fs14.writeFileSync(hookPath, content);
+    fs15.writeFileSync(hookPath, content);
   }
   return { removed: true, notFound: false };
 }
 
 // src/lib/learning-hooks.ts
-import fs15 from "fs";
+import fs16 from "fs";
 import path13 from "path";
 var SETTINGS_PATH2 = path13.join(".claude", "settings.json");
 var HOOK_CONFIGS = [
@@ -2356,17 +2423,17 @@ var HOOK_CONFIGS = [
   }
 ];
 function readSettings2() {
-  if (!fs15.existsSync(SETTINGS_PATH2)) return {};
+  if (!fs16.existsSync(SETTINGS_PATH2)) return {};
   try {
-    return JSON.parse(fs15.readFileSync(SETTINGS_PATH2, "utf-8"));
+    return JSON.parse(fs16.readFileSync(SETTINGS_PATH2, "utf-8"));
   } catch {
     return {};
   }
 }
 function writeSettings2(settings) {
   const dir = path13.dirname(SETTINGS_PATH2);
-  if (!fs15.existsSync(dir)) fs15.mkdirSync(dir, { recursive: true });
-  fs15.writeFileSync(SETTINGS_PATH2, JSON.stringify(settings, null, 2));
+  if (!fs16.existsSync(dir)) fs16.mkdirSync(dir, { recursive: true });
+  fs16.writeFileSync(SETTINGS_PATH2, JSON.stringify(settings, null, 2));
 }
 function hasLearningHook(matchers, command) {
   return matchers.some((entry) => entry.hooks?.some((h) => h.command === command));
@@ -2423,7 +2490,7 @@ function removeLearningHooks() {
 
 // src/lib/state.ts
 init_constants();
-import fs16 from "fs";
+import fs17 from "fs";
 import path14 from "path";
 import { execSync as execSync6 } from "child_process";
 var STATE_FILE = path14.join(CALIBER_DIR, ".caliber-state.json");
@@ -2437,8 +2504,8 @@ function normalizeTargetAgent(value) {
 }
 function readState() {
   try {
-    if (!fs16.existsSync(STATE_FILE)) return null;
-    const raw = JSON.parse(fs16.readFileSync(STATE_FILE, "utf-8"));
+    if (!fs17.existsSync(STATE_FILE)) return null;
+    const raw = JSON.parse(fs17.readFileSync(STATE_FILE, "utf-8"));
     if (raw.targetAgent) raw.targetAgent = normalizeTargetAgent(raw.targetAgent);
     return raw;
   } catch {
@@ -2446,10 +2513,10 @@ function readState() {
   }
 }
 function writeState(state) {
-  if (!fs16.existsSync(CALIBER_DIR)) {
-    fs16.mkdirSync(CALIBER_DIR, { recursive: true });
+  if (!fs17.existsSync(CALIBER_DIR)) {
+    fs17.mkdirSync(CALIBER_DIR, { recursive: true });
   }
-  fs16.writeFileSync(STATE_FILE, JSON.stringify(state, null, 2));
+  fs17.writeFileSync(STATE_FILE, JSON.stringify(state, null, 2));
 }
 function getCurrentHeadSha() {
   try {
@@ -3670,22 +3737,22 @@ function checkBonus(dir) {
 
 // src/scoring/dismissed.ts
 init_constants();
-import fs17 from "fs";
+import fs18 from "fs";
 import path15 from "path";
 var DISMISSED_FILE = path15.join(CALIBER_DIR, "dismissed-checks.json");
 function readDismissedChecks() {
   try {
-    if (!fs17.existsSync(DISMISSED_FILE)) return [];
-    return JSON.parse(fs17.readFileSync(DISMISSED_FILE, "utf-8"));
+    if (!fs18.existsSync(DISMISSED_FILE)) return [];
+    return JSON.parse(fs18.readFileSync(DISMISSED_FILE, "utf-8"));
   } catch {
     return [];
   }
 }
 function writeDismissedChecks(checks) {
-  if (!fs17.existsSync(CALIBER_DIR)) {
-    fs17.mkdirSync(CALIBER_DIR, { recursive: true });
+  if (!fs18.existsSync(CALIBER_DIR)) {
+    fs18.mkdirSync(CALIBER_DIR, { recursive: true });
   }
-  fs17.writeFileSync(DISMISSED_FILE, JSON.stringify(checks, null, 2) + "\n");
+  fs18.writeFileSync(DISMISSED_FILE, JSON.stringify(checks, null, 2) + "\n");
 }
 function getDismissedIds() {
   return new Set(readDismissedChecks().map((c) => c.id));
@@ -3876,7 +3943,7 @@ function displayScoreDelta(before, after) {
 import chalk4 from "chalk";
 import ora from "ora";
 import readline3 from "readline";
-import fs18 from "fs";
+import fs19 from "fs";
 import path16 from "path";
 
 // src/mcp/search.ts
@@ -4229,7 +4296,7 @@ async function discoverAndInstallMcps(targetAgent, fingerprint, dir) {
   }
   if (targetAgent.includes("cursor")) {
     const cursorDir = path16.join(dir, ".cursor");
-    if (!fs18.existsSync(cursorDir)) fs18.mkdirSync(cursorDir, { recursive: true });
+    if (!fs19.existsSync(cursorDir)) fs19.mkdirSync(cursorDir, { recursive: true });
     writeMcpJson(path16.join(cursorDir, "mcp.json"), mcpServers);
   }
   return { installed: installedNames.length, names: installedNames };
@@ -4237,14 +4304,14 @@ async function discoverAndInstallMcps(targetAgent, fingerprint, dir) {
 function writeMcpJson(filePath, mcpServers) {
   let existing = {};
   try {
-    if (fs18.existsSync(filePath)) {
-      const parsed = JSON.parse(fs18.readFileSync(filePath, "utf-8"));
+    if (fs19.existsSync(filePath)) {
+      const parsed = JSON.parse(fs19.readFileSync(filePath, "utf-8"));
       if (parsed.mcpServers) existing = parsed.mcpServers;
     }
   } catch {
   }
   const merged = { ...existing, ...mcpServers };
-  fs18.writeFileSync(filePath, JSON.stringify({ mcpServers: merged }, null, 2) + "\n");
+  fs19.writeFileSync(filePath, JSON.stringify({ mcpServers: merged }, null, 2) + "\n");
 }
 function getExistingMcpNames(fingerprint, targetAgent) {
   const names = [];
@@ -4859,8 +4926,8 @@ async function openReview(method, stagedFiles) {
     return;
   }
   const fileInfos = stagedFiles.map((file) => {
-    const proposed = fs19.readFileSync(file.proposedPath, "utf-8");
-    const current = file.currentPath ? fs19.readFileSync(file.currentPath, "utf-8") : "";
+    const proposed = fs20.readFileSync(file.proposedPath, "utf-8");
+    const current = file.currentPath ? fs20.readFileSync(file.currentPath, "utf-8") : "";
     const patch = createTwoFilesPatch(
       file.isNew ? "/dev/null" : file.relativePath,
       file.relativePath,
@@ -5043,7 +5110,7 @@ function printSetupSummary(setup) {
   };
   if (claude) {
     if (claude.claudeMd) {
-      const icon = fs19.existsSync("CLAUDE.md") ? chalk5.yellow("~") : chalk5.green("+");
+      const icon = fs20.existsSync("CLAUDE.md") ? chalk5.yellow("~") : chalk5.green("+");
       const desc = getDescription("CLAUDE.md");
       console.log(`  ${icon} ${chalk5.bold("CLAUDE.md")}`);
       if (desc) console.log(chalk5.dim(`    ${desc}`));
@@ -5053,7 +5120,7 @@ function printSetupSummary(setup) {
     if (Array.isArray(skills) && skills.length > 0) {
       for (const skill of skills) {
         const skillPath = `.claude/skills/${skill.name}/SKILL.md`;
-        const icon = fs19.existsSync(skillPath) ? chalk5.yellow("~") : chalk5.green("+");
+        const icon = fs20.existsSync(skillPath) ? chalk5.yellow("~") : chalk5.green("+");
         const desc = getDescription(skillPath);
         console.log(`  ${icon} ${chalk5.bold(skillPath)}`);
         console.log(chalk5.dim(`    ${desc || skill.description || skill.name}`));
@@ -5064,7 +5131,7 @@ function printSetupSummary(setup) {
   const codex = setup.codex;
   if (codex) {
     if (codex.agentsMd) {
-      const icon = fs19.existsSync("AGENTS.md") ? chalk5.yellow("~") : chalk5.green("+");
+      const icon = fs20.existsSync("AGENTS.md") ? chalk5.yellow("~") : chalk5.green("+");
       const desc = getDescription("AGENTS.md");
       console.log(`  ${icon} ${chalk5.bold("AGENTS.md")}`);
       if (desc) console.log(chalk5.dim(`    ${desc}`));
@@ -5074,7 +5141,7 @@ function printSetupSummary(setup) {
     if (Array.isArray(codexSkills) && codexSkills.length > 0) {
       for (const skill of codexSkills) {
         const skillPath = `.agents/skills/${skill.name}/SKILL.md`;
-        const icon = fs19.existsSync(skillPath) ? chalk5.yellow("~") : chalk5.green("+");
+        const icon = fs20.existsSync(skillPath) ? chalk5.yellow("~") : chalk5.green("+");
         const desc = getDescription(skillPath);
         console.log(`  ${icon} ${chalk5.bold(skillPath)}`);
         console.log(chalk5.dim(`    ${desc || skill.description || skill.name}`));
@@ -5084,7 +5151,7 @@ function printSetupSummary(setup) {
   }
   if (cursor) {
     if (cursor.cursorrules) {
-      const icon = fs19.existsSync(".cursorrules") ? chalk5.yellow("~") : chalk5.green("+");
+      const icon = fs20.existsSync(".cursorrules") ? chalk5.yellow("~") : chalk5.green("+");
       const desc = getDescription(".cursorrules");
       console.log(`  ${icon} ${chalk5.bold(".cursorrules")}`);
       if (desc) console.log(chalk5.dim(`    ${desc}`));
@@ -5094,7 +5161,7 @@ function printSetupSummary(setup) {
     if (Array.isArray(cursorSkills) && cursorSkills.length > 0) {
       for (const skill of cursorSkills) {
         const skillPath = `.cursor/skills/${skill.name}/SKILL.md`;
-        const icon = fs19.existsSync(skillPath) ? chalk5.yellow("~") : chalk5.green("+");
+        const icon = fs20.existsSync(skillPath) ? chalk5.yellow("~") : chalk5.green("+");
         const desc = getDescription(skillPath);
         console.log(`  ${icon} ${chalk5.bold(skillPath)}`);
         console.log(chalk5.dim(`    ${desc || skill.description || skill.name}`));
@@ -5105,7 +5172,7 @@ function printSetupSummary(setup) {
     if (Array.isArray(rules) && rules.length > 0) {
       for (const rule of rules) {
         const rulePath = `.cursor/rules/${rule.filename}`;
-        const icon = fs19.existsSync(rulePath) ? chalk5.yellow("~") : chalk5.green("+");
+        const icon = fs20.existsSync(rulePath) ? chalk5.yellow("~") : chalk5.green("+");
         const desc = getDescription(rulePath);
         console.log(`  ${icon} ${chalk5.bold(rulePath)}`);
         if (desc) {
@@ -5118,7 +5185,7 @@ function printSetupSummary(setup) {
       }
     }
   }
-  if (!codex && !fs19.existsSync("AGENTS.md")) {
+  if (!codex && !fs20.existsSync("AGENTS.md")) {
     console.log(`  ${chalk5.green("+")} ${chalk5.bold("AGENTS.md")}`);
     console.log(chalk5.dim("    Cross-agent coordination file"));
     console.log("");
@@ -5133,21 +5200,12 @@ function printSetupSummary(setup) {
   console.log(`  ${chalk5.green("+")} ${chalk5.dim("new")}  ${chalk5.yellow("~")} ${chalk5.dim("modified")}  ${chalk5.red("-")} ${chalk5.dim("removed")}`);
   console.log("");
 }
-function buildSkillContent(skill) {
-  const frontmatter = `---
-name: ${skill.name}
-description: ${skill.description}
----
-
-`;
-  return frontmatter + skill.content;
-}
 function ensurePermissions() {
   const settingsPath = ".claude/settings.json";
   let settings = {};
   try {
-    if (fs19.existsSync(settingsPath)) {
-      settings = JSON.parse(fs19.readFileSync(settingsPath, "utf-8"));
+    if (fs20.existsSync(settingsPath)) {
+      settings = JSON.parse(fs20.readFileSync(settingsPath, "utf-8"));
     }
   } catch {
   }
@@ -5161,64 +5219,8 @@ function ensurePermissions() {
     "Bash(git *)"
   ];
   settings.permissions = permissions;
-  if (!fs19.existsSync(".claude")) fs19.mkdirSync(".claude", { recursive: true });
-  fs19.writeFileSync(settingsPath, JSON.stringify(settings, null, 2) + "\n");
-}
-function collectSetupFiles(setup) {
-  const files = [];
-  const claude = setup.claude;
-  const cursor = setup.cursor;
-  const codex = setup.codex;
-  if (claude) {
-    if (claude.claudeMd) files.push({ path: "CLAUDE.md", content: claude.claudeMd });
-    const skills = claude.skills;
-    if (Array.isArray(skills)) {
-      for (const skill of skills) {
-        files.push({ path: `.claude/skills/${skill.name}/SKILL.md`, content: buildSkillContent(skill) });
-      }
-    }
-  }
-  if (codex) {
-    if (codex.agentsMd) files.push({ path: "AGENTS.md", content: codex.agentsMd });
-    const codexSkills = codex.skills;
-    if (Array.isArray(codexSkills)) {
-      for (const skill of codexSkills) {
-        files.push({ path: `.agents/skills/${skill.name}/SKILL.md`, content: buildSkillContent(skill) });
-      }
-    }
-  }
-  if (cursor) {
-    if (cursor.cursorrules) files.push({ path: ".cursorrules", content: cursor.cursorrules });
-    const cursorSkills = cursor.skills;
-    if (Array.isArray(cursorSkills)) {
-      for (const skill of cursorSkills) {
-        files.push({ path: `.cursor/skills/${skill.name}/SKILL.md`, content: buildSkillContent(skill) });
-      }
-    }
-    const rules = cursor.rules;
-    if (Array.isArray(rules)) {
-      for (const rule of rules) {
-        files.push({ path: `.cursor/rules/${rule.filename}`, content: rule.content });
-      }
-    }
-  }
-  const hasCodexAgentsMd = codex && codex.agentsMd;
-  if (!fs19.existsSync("AGENTS.md") && !hasCodexAgentsMd) {
-    const agentRefs = [];
-    if (claude) agentRefs.push("See `CLAUDE.md` for Claude Code configuration.");
-    if (cursor) agentRefs.push("See `.cursor/rules/` for Cursor rules.");
-    if (agentRefs.length === 0) agentRefs.push("See CLAUDE.md and .cursor/rules/ for agent configurations.");
-    files.push({
-      path: "AGENTS.md",
-      content: `# AGENTS.md
-
-This project uses AI coding agents configured by [Caliber](https://github.com/rely-ai-org/caliber).
-
-${agentRefs.join(" ")}
-`
-    });
-  }
-  return files;
+  if (!fs20.existsSync(".claude")) fs20.mkdirSync(".claude", { recursive: true });
+  fs20.writeFileSync(settingsPath, JSON.stringify(settings, null, 2) + "\n");
 }
 
 // src/commands/undo.ts
@@ -5254,7 +5256,7 @@ function undoCommand() {
 
 // src/commands/status.ts
 import chalk7 from "chalk";
-import fs20 from "fs";
+import fs21 from "fs";
 async function statusCommand(options) {
   const config = loadConfig();
   const manifest = readManifest();
@@ -5280,7 +5282,7 @@ async function statusCommand(options) {
   }
   console.log(`  Files managed: ${chalk7.cyan(manifest.entries.length.toString())}`);
   for (const entry of manifest.entries) {
-    const exists = fs20.existsSync(entry.path);
+    const exists = fs21.existsSync(entry.path);
     const icon = exists ? chalk7.green("\u2713") : chalk7.red("\u2717");
     console.log(`    ${icon} ${entry.path} (${entry.action})`);
   }
@@ -5290,11 +5292,11 @@ async function statusCommand(options) {
 // src/commands/regenerate.ts
 import chalk8 from "chalk";
 import ora4 from "ora";
-import confirm from "@inquirer/confirm";
+import select3 from "@inquirer/select";
 async function regenerateCommand(options) {
   const config = loadConfig();
   if (!config) {
-    console.log(chalk8.red("No LLM provider configured. Run ") + chalk8.hex("#83D1EB")("caliber config") + chalk8.red(" (e.g. choose Cursor) or set ANTHROPIC_API_KEY."));
+    console.log(chalk8.red("No LLM provider configured. Run ") + chalk8.hex("#83D1EB")("caliber config") + chalk8.red(" first."));
     throw new Error("__exit__");
   }
   const manifest = readManifest();
@@ -5302,16 +5304,19 @@ async function regenerateCommand(options) {
     console.log(chalk8.yellow("No existing setup found. Run ") + chalk8.hex("#83D1EB")("caliber onboard") + chalk8.yellow(" first."));
     throw new Error("__exit__");
   }
-  const spinner = ora4("Re-analyzing project...").start();
+  const targetAgent = readState()?.targetAgent ?? ["claude", "cursor"];
+  const spinner = ora4("Analyzing project...").start();
   const fingerprint = collectFingerprint(process.cwd());
-  spinner.succeed("Project re-analyzed");
+  await enrichFingerprintWithLLM(fingerprint, process.cwd());
+  spinner.succeed("Project analyzed");
+  const baselineScore = computeLocalScore(process.cwd(), targetAgent);
+  displayScoreSummary(baselineScore);
   const genSpinner = ora4("Regenerating setup...").start();
-  const genMessages = new SpinnerMessages(genSpinner, GENERATION_MESSAGES);
+  const genMessages = new SpinnerMessages(genSpinner, GENERATION_MESSAGES, { showElapsedTime: true });
   genMessages.start();
   let generatedSetup = null;
   try {
-    const targetAgent = readState()?.targetAgent ?? ["claude", "cursor"];
-    const result2 = await generateSetup(
+    const result = await generateSetup(
       fingerprint,
       targetAgent,
       void 0,
@@ -5328,7 +5333,7 @@ async function regenerateCommand(options) {
         }
       }
     );
-    if (!generatedSetup) generatedSetup = result2.setup;
+    if (!generatedSetup) generatedSetup = result.setup;
   } catch (err) {
     genMessages.stop();
     const msg = err instanceof Error ? err.message : "Unknown error";
@@ -5341,23 +5346,81 @@ async function regenerateCommand(options) {
     throw new Error("__exit__");
   }
   genSpinner.succeed("Setup regenerated");
+  const setupFiles = collectSetupFiles(generatedSetup);
+  const staged = stageFiles(setupFiles, process.cwd());
+  const totalChanges = staged.newFiles + staged.modifiedFiles;
+  console.log(chalk8.dim(`
+  ${chalk8.green(`${staged.newFiles} new`)} / ${chalk8.yellow(`${staged.modifiedFiles} modified`)} file${totalChanges !== 1 ? "s" : ""}
+`));
+  if (totalChanges === 0) {
+    console.log(chalk8.dim("  No changes needed \u2014 your configs are already up to date.\n"));
+    cleanupStaging();
+    return;
+  }
   if (options.dryRun) {
-    console.log(chalk8.yellow("\n[Dry run] Would write:"));
-    console.log(JSON.stringify(generatedSetup, null, 2));
+    console.log(chalk8.yellow("[Dry run] Would write:"));
+    for (const f of staged.stagedFiles) {
+      console.log(`  ${f.isNew ? chalk8.green("+") : chalk8.yellow("~")} ${f.relativePath}`);
+    }
+    cleanupStaging();
     return;
   }
-  const shouldApply = await confirm({ message: "Apply regenerated setup?", default: true });
-  if (!shouldApply) {
-    console.log(chalk8.dim("Regeneration cancelled."));
+  const action = await select3({
+    message: "Apply regenerated setup?",
+    choices: [
+      { name: "Accept and apply", value: "accept" },
+      { name: "Decline", value: "decline" }
+    ]
+  });
+  cleanupStaging();
+  if (action === "decline") {
+    console.log(chalk8.dim("Regeneration cancelled. No files were modified."));
     return;
   }
-  const writeSpinner = ora4("Updating config files...").start();
-  const result = writeSetup(generatedSetup);
-  writeSpinner.succeed("Config files updated");
-  for (const file of result.written) {
-    console.log(`  ${chalk8.green("\u2713")} ${file}`);
+  const writeSpinner = ora4("Writing config files...").start();
+  try {
+    const result = writeSetup(generatedSetup);
+    writeSpinner.succeed("Config files written");
+    for (const file of result.written) {
+      console.log(`  ${chalk8.green("\u2713")} ${file}`);
+    }
+    if (result.deleted.length > 0) {
+      for (const file of result.deleted) {
+        console.log(`  ${chalk8.red("\u2717")} ${file}`);
+      }
+    }
+    if (result.backupDir) {
+      console.log(chalk8.dim(`
+  Backups saved to ${result.backupDir}`));
+    }
+  } catch (err) {
+    writeSpinner.fail("Failed to write files");
+    console.error(chalk8.red(err instanceof Error ? err.message : "Unknown error"));
+    throw new Error("__exit__");
   }
-  console.log("");
+  const sha = getCurrentHeadSha();
+  writeState({
+    lastRefreshSha: sha ?? "",
+    lastRefreshTimestamp: (/* @__PURE__ */ new Date()).toISOString(),
+    targetAgent
+  });
+  const afterScore = computeLocalScore(process.cwd(), targetAgent);
+  if (afterScore.score < baselineScore.score) {
+    console.log("");
+    console.log(chalk8.yellow(`  Score would drop from ${baselineScore.score} to ${afterScore.score} \u2014 reverting changes.`));
+    try {
+      const { restored, removed } = undoSetup();
+      if (restored.length > 0 || removed.length > 0) {
+        console.log(chalk8.dim(`  Reverted ${restored.length + removed.length} file${restored.length + removed.length === 1 ? "" : "s"} from backup.`));
+      }
+    } catch {
+    }
+    console.log(chalk8.dim("  Run ") + chalk8.hex("#83D1EB")("caliber onboard --force") + chalk8.dim(" to override.\n"));
+    return;
+  }
+  displayScoreDelta(baselineScore, afterScore);
+  console.log(chalk8.bold.green("  Regeneration complete!"));
+  console.log(chalk8.dim("  Run ") + chalk8.hex("#83D1EB")("caliber undo") + chalk8.dim(" to revert changes.\n"));
 }
 
 // src/commands/recommend.ts
@@ -5367,13 +5430,13 @@ import { mkdirSync, readFileSync as readFileSync7, readdirSync as readdirSync5,
 import { join as join8, dirname as dirname2 } from "path";
 
 // src/scanner/index.ts
-import fs21 from "fs";
+import fs22 from "fs";
 import path17 from "path";
 import crypto2 from "crypto";
 function scanLocalState(dir) {
   const items = [];
   const claudeMdPath = path17.join(dir, "CLAUDE.md");
-  if (fs21.existsSync(claudeMdPath)) {
+  if (fs22.existsSync(claudeMdPath)) {
     items.push({
       type: "rule",
       platform: "claude",
@@ -5383,8 +5446,8 @@ function scanLocalState(dir) {
     });
   }
   const skillsDir = path17.join(dir, ".claude", "skills");
-  if (fs21.existsSync(skillsDir)) {
-    for (const file of fs21.readdirSync(skillsDir).filter((f) => f.endsWith(".md"))) {
+  if (fs22.existsSync(skillsDir)) {
+    for (const file of fs22.readdirSync(skillsDir).filter((f) => f.endsWith(".md"))) {
       const filePath = path17.join(skillsDir, file);
       items.push({
         type: "skill",
@@ -5396,9 +5459,9 @@ function scanLocalState(dir) {
     }
   }
   const mcpJsonPath = path17.join(dir, ".mcp.json");
-  if (fs21.existsSync(mcpJsonPath)) {
+  if (fs22.existsSync(mcpJsonPath)) {
     try {
-      const mcpJson = JSON.parse(fs21.readFileSync(mcpJsonPath, "utf-8"));
+      const mcpJson = JSON.parse(fs22.readFileSync(mcpJsonPath, "utf-8"));
       if (mcpJson.mcpServers) {
         for (const name of Object.keys(mcpJson.mcpServers)) {
           items.push({
@@ -5414,7 +5477,7 @@ function scanLocalState(dir) {
     }
   }
   const agentsMdPath = path17.join(dir, "AGENTS.md");
-  if (fs21.existsSync(agentsMdPath)) {
+  if (fs22.existsSync(agentsMdPath)) {
     items.push({
       type: "rule",
       platform: "codex",
@@ -5424,11 +5487,11 @@ function scanLocalState(dir) {
     });
   }
   const codexSkillsDir = path17.join(dir, ".agents", "skills");
-  if (fs21.existsSync(codexSkillsDir)) {
+  if (fs22.existsSync(codexSkillsDir)) {
     try {
-      for (const name of fs21.readdirSync(codexSkillsDir)) {
+      for (const name of fs22.readdirSync(codexSkillsDir)) {
         const skillFile = path17.join(codexSkillsDir, name, "SKILL.md");
-        if (fs21.existsSync(skillFile)) {
+        if (fs22.existsSync(skillFile)) {
           items.push({
             type: "skill",
             platform: "codex",
@@ -5442,7 +5505,7 @@ function scanLocalState(dir) {
     }
   }
   const cursorrulesPath = path17.join(dir, ".cursorrules");
-  if (fs21.existsSync(cursorrulesPath)) {
+  if (fs22.existsSync(cursorrulesPath)) {
     items.push({
       type: "rule",
       platform: "cursor",
@@ -5452,8 +5515,8 @@ function scanLocalState(dir) {
     });
   }
   const cursorRulesDir = path17.join(dir, ".cursor", "rules");
-  if (fs21.existsSync(cursorRulesDir)) {
-    for (const file of fs21.readdirSync(cursorRulesDir).filter((f) => f.endsWith(".mdc"))) {
+  if (fs22.existsSync(cursorRulesDir)) {
+    for (const file of fs22.readdirSync(cursorRulesDir).filter((f) => f.endsWith(".mdc"))) {
       const filePath = path17.join(cursorRulesDir, file);
       items.push({
         type: "rule",
@@ -5465,11 +5528,11 @@ function scanLocalState(dir) {
     }
   }
   const cursorSkillsDir = path17.join(dir, ".cursor", "skills");
-  if (fs21.existsSync(cursorSkillsDir)) {
+  if (fs22.existsSync(cursorSkillsDir)) {
     try {
-      for (const name of fs21.readdirSync(cursorSkillsDir)) {
+      for (const name of fs22.readdirSync(cursorSkillsDir)) {
         const skillFile = path17.join(cursorSkillsDir, name, "SKILL.md");
-        if (fs21.existsSync(skillFile)) {
+        if (fs22.existsSync(skillFile)) {
           items.push({
             type: "skill",
             platform: "cursor",
@@ -5483,9 +5546,9 @@ function scanLocalState(dir) {
     }
   }
   const cursorMcpPath = path17.join(dir, ".cursor", "mcp.json");
-  if (fs21.existsSync(cursorMcpPath)) {
+  if (fs22.existsSync(cursorMcpPath)) {
     try {
-      const mcpJson = JSON.parse(fs21.readFileSync(cursorMcpPath, "utf-8"));
+      const mcpJson = JSON.parse(fs22.readFileSync(cursorMcpPath, "utf-8"));
       if (mcpJson.mcpServers) {
         for (const name of Object.keys(mcpJson.mcpServers)) {
           items.push({
@@ -5503,7 +5566,7 @@ function scanLocalState(dir) {
   return items;
 }
 function hashFile(filePath) {
-  const text = fs21.readFileSync(filePath, "utf-8");
+  const text = fs22.readFileSync(filePath, "utf-8");
   return crypto2.createHash("sha256").update(JSON.stringify({ text })).digest("hex");
 }
 function hashJson(obj) {
@@ -6078,13 +6141,13 @@ async function scoreCommand(options) {
   } else if (result.score < 70) {
     console.log(chalk10.gray("  Run ") + chalk10.hex("#83D1EB")("caliber onboard") + chalk10.gray(" to improve your setup."));
   } else {
-    console.log(chalk10.green("  Looking good!") + chalk10.gray(" Run ") + chalk10.hex("#83D1EB")("caliber update") + chalk10.gray(" to keep it fresh."));
+    console.log(chalk10.green("  Looking good!") + chalk10.gray(" Run ") + chalk10.hex("#83D1EB")("caliber regenerate") + chalk10.gray(" to rebuild from scratch."));
   }
   console.log("");
 }
 
 // src/commands/refresh.ts
-import fs23 from "fs";
+import fs24 from "fs";
 import path19 from "path";
 import chalk11 from "chalk";
 import ora6 from "ora";
@@ -6162,37 +6225,37 @@ function collectDiff(lastSha) {
 }
 
 // src/writers/refresh.ts
-import fs22 from "fs";
+import fs23 from "fs";
 import path18 from "path";
 function writeRefreshDocs(docs) {
   const written = [];
   if (docs.claudeMd) {
-    fs22.writeFileSync("CLAUDE.md", docs.claudeMd);
+    fs23.writeFileSync("CLAUDE.md", docs.claudeMd);
     written.push("CLAUDE.md");
   }
   if (docs.readmeMd) {
-    fs22.writeFileSync("README.md", docs.readmeMd);
+    fs23.writeFileSync("README.md", docs.readmeMd);
     written.push("README.md");
   }
   if (docs.cursorrules) {
-    fs22.writeFileSync(".cursorrules", docs.cursorrules);
+    fs23.writeFileSync(".cursorrules", docs.cursorrules);
     written.push(".cursorrules");
   }
   if (docs.cursorRules) {
     const rulesDir = path18.join(".cursor", "rules");
-    if (!fs22.existsSync(rulesDir)) fs22.mkdirSync(rulesDir, { recursive: true });
+    if (!fs23.existsSync(rulesDir)) fs23.mkdirSync(rulesDir, { recursive: true });
     for (const rule of docs.cursorRules) {
       const filePath = path18.join(rulesDir, rule.filename);
-      fs22.writeFileSync(filePath, rule.content);
+      fs23.writeFileSync(filePath, rule.content);
       written.push(filePath);
     }
   }
   if (docs.claudeSkills) {
     const skillsDir = path18.join(".claude", "skills");
-    if (!fs22.existsSync(skillsDir)) fs22.mkdirSync(skillsDir, { recursive: true });
+    if (!fs23.existsSync(skillsDir)) fs23.mkdirSync(skillsDir, { recursive: true });
     for (const skill of docs.claudeSkills) {
       const filePath = path18.join(skillsDir, skill.filename);
-      fs22.writeFileSync(filePath, skill.content);
+      fs23.writeFileSync(filePath, skill.content);
       written.push(filePath);
     }
   }
@@ -6269,11 +6332,11 @@ function log(quiet, ...args) {
 function discoverGitRepos(parentDir) {
   const repos = [];
   try {
-    const entries = fs23.readdirSync(parentDir, { withFileTypes: true });
+    const entries = fs24.readdirSync(parentDir, { withFileTypes: true });
     for (const entry of entries) {
       if (!entry.isDirectory() || entry.name.startsWith(".")) continue;
       const childPath = path19.join(parentDir, entry.name);
-      if (fs23.existsSync(path19.join(childPath, ".git"))) {
+      if (fs24.existsSync(path19.join(childPath, ".git"))) {
         repos.push(childPath);
       }
     }
@@ -6620,7 +6683,7 @@ function readStdin() {
 
 // src/learner/storage.ts
 init_constants();
-import fs24 from "fs";
+import fs25 from "fs";
 import path20 from "path";
 var MAX_RESPONSE_LENGTH = 2e3;
 var DEFAULT_STATE = {
@@ -6629,8 +6692,8 @@ var DEFAULT_STATE = {
   lastAnalysisTimestamp: null
 };
 function ensureLearningDir() {
-  if (!fs24.existsSync(LEARNING_DIR)) {
-    fs24.mkdirSync(LEARNING_DIR, { recursive: true });
+  if (!fs25.existsSync(LEARNING_DIR)) {
+    fs25.mkdirSync(LEARNING_DIR, { recursive: true });
   }
 }
 function sessionFilePath() {
@@ -6648,49 +6711,49 @@ function appendEvent(event) {
   ensureLearningDir();
   const truncated = { ...event, tool_response: truncateResponse(event.tool_response) };
   const filePath = sessionFilePath();
-  fs24.appendFileSync(filePath, JSON.stringify(truncated) + "\n");
+  fs25.appendFileSync(filePath, JSON.stringify(truncated) + "\n");
   const count = getEventCount();
   if (count > LEARNING_MAX_EVENTS) {
-    const lines = fs24.readFileSync(filePath, "utf-8").split("\n").filter(Boolean);
+    const lines = fs25.readFileSync(filePath, "utf-8").split("\n").filter(Boolean);
     const kept = lines.slice(lines.length - LEARNING_MAX_EVENTS);
-    fs24.writeFileSync(filePath, kept.join("\n") + "\n");
+    fs25.writeFileSync(filePath, kept.join("\n") + "\n");
   }
 }
 function readAllEvents() {
   const filePath = sessionFilePath();
-  if (!fs24.existsSync(filePath)) return [];
-  const lines = fs24.readFileSync(filePath, "utf-8").split("\n").filter(Boolean);
+  if (!fs25.existsSync(filePath)) return [];
+  const lines = fs25.readFileSync(filePath, "utf-8").split("\n").filter(Boolean);
   return lines.map((line) => JSON.parse(line));
 }
 function getEventCount() {
   const filePath = sessionFilePath();
-  if (!fs24.existsSync(filePath)) return 0;
-  const content = fs24.readFileSync(filePath, "utf-8");
+  if (!fs25.existsSync(filePath)) return 0;
+  const content = fs25.readFileSync(filePath, "utf-8");
   return content.split("\n").filter(Boolean).length;
 }
 function clearSession() {
   const filePath = sessionFilePath();
-  if (fs24.existsSync(filePath)) fs24.unlinkSync(filePath);
+  if (fs25.existsSync(filePath)) fs25.unlinkSync(filePath);
 }
 function readState2() {
   const filePath = stateFilePath();
-  if (!fs24.existsSync(filePath)) return { ...DEFAULT_STATE };
+  if (!fs25.existsSync(filePath)) return { ...DEFAULT_STATE };
   try {
-    return JSON.parse(fs24.readFileSync(filePath, "utf-8"));
+    return JSON.parse(fs25.readFileSync(filePath, "utf-8"));
   } catch {
     return { ...DEFAULT_STATE };
   }
 }
 function writeState2(state) {
   ensureLearningDir();
-  fs24.writeFileSync(stateFilePath(), JSON.stringify(state, null, 2));
+  fs25.writeFileSync(stateFilePath(), JSON.stringify(state, null, 2));
 }
 function resetState() {
   writeState2({ ...DEFAULT_STATE });
 }
 
 // src/learner/writer.ts
-import fs25 from "fs";
+import fs26 from "fs";
 import path21 from "path";
 var LEARNED_START = "<!-- caliber:learned -->";
 var LEARNED_END = "<!-- /caliber:learned -->";
@@ -6711,8 +6774,8 @@ function writeLearnedContent(update) {
 function writeLearnedSection(content) {
   const claudeMdPath = "CLAUDE.md";
   let existing = "";
-  if (fs25.existsSync(claudeMdPath)) {
-    existing = fs25.readFileSync(claudeMdPath, "utf-8");
+  if (fs26.existsSync(claudeMdPath)) {
+    existing = fs26.readFileSync(claudeMdPath, "utf-8");
   }
   const section = `${LEARNED_START}
 ${content}
@@ -6726,15 +6789,15 @@ ${LEARNED_END}`;
     const separator = existing.endsWith("\n") || existing === "" ? "" : "\n";
     updated = existing + separator + "\n" + section + "\n";
   }
-  fs25.writeFileSync(claudeMdPath, updated);
+  fs26.writeFileSync(claudeMdPath, updated);
 }
 function writeLearnedSkill(skill) {
   const skillDir = path21.join(".claude", "skills", skill.name);
-  if (!fs25.existsSync(skillDir)) fs25.mkdirSync(skillDir, { recursive: true });
+  if (!fs26.existsSync(skillDir)) fs26.mkdirSync(skillDir, { recursive: true });
   const skillPath = path21.join(skillDir, "SKILL.md");
-  if (!skill.isNew && fs25.existsSync(skillPath)) {
-    const existing = fs25.readFileSync(skillPath, "utf-8");
-    fs25.writeFileSync(skillPath, existing.trimEnd() + "\n\n" + skill.content);
+  if (!skill.isNew && fs26.existsSync(skillPath)) {
+    const existing = fs26.readFileSync(skillPath, "utf-8");
+    fs26.writeFileSync(skillPath, existing.trimEnd() + "\n\n" + skill.content);
   } else {
     const frontmatter = [
       "---",
@@ -6743,14 +6806,14 @@ function writeLearnedSkill(skill) {
       "---",
       ""
     ].join("\n");
-    fs25.writeFileSync(skillPath, frontmatter + skill.content);
+    fs26.writeFileSync(skillPath, frontmatter + skill.content);
   }
   return skillPath;
 }
 function readLearnedSection() {
   const claudeMdPath = "CLAUDE.md";
-  if (!fs25.existsSync(claudeMdPath)) return null;
-  const content = fs25.readFileSync(claudeMdPath, "utf-8");
+  if (!fs26.existsSync(claudeMdPath)) return null;
+  const content = fs26.readFileSync(claudeMdPath, "utf-8");
   const startIdx = content.indexOf(LEARNED_START);
   const endIdx = content.indexOf(LEARNED_END);
   if (startIdx === -1 || endIdx === -1) return null;
@@ -6936,7 +6999,7 @@ Learned items in CLAUDE.md: ${chalk14.cyan(String(lineCount))}`);
 // src/cli.ts
 var __dirname = path22.dirname(fileURLToPath(import.meta.url));
 var pkg = JSON.parse(
-  fs26.readFileSync(path22.resolve(__dirname, "..", "package.json"), "utf-8")
+  fs27.readFileSync(path22.resolve(__dirname, "..", "package.json"), "utf-8")
 );
 var program = new Command();
 var displayVersion = process.env.CALIBER_LOCAL ? `${pkg.version}-local` : pkg.version;
@@ -6955,7 +7018,7 @@ function parseAgentOption(value) {
 program.command("onboard").alias("init").description("Onboard your project for AI-assisted development").option("--agent <type>", "Target agents (comma-separated): claude, cursor, codex", parseAgentOption).option("--dry-run", "Preview changes without writing files").option("--force", "Overwrite existing setup without prompting").action(initCommand);
 program.command("undo").description("Revert all config changes made by Caliber").action(undoCommand);
 program.command("status").description("Show current Caliber setup status").option("--json", "Output as JSON").action(statusCommand);
-program.command("regenerate").alias("regen").alias("re").alias("update").description("Re-analyze project and regenerate setup").option("--dry-run", "Preview changes without writing files").action(regenerateCommand);
+program.command("regenerate").alias("regen").alias("re").description("Re-analyze project and regenerate setup").option("--dry-run", "Preview changes without writing files").action(regenerateCommand);
 program.command("config").description("Configure LLM provider, API key, and model").action(configCommand);
 program.command("recommend").description("Discover and install skill recommendations").option("--generate", "Force fresh recommendation search").action(recommendCommand);
 program.command("score").description("Score your current agent config setup (deterministic, no network)").option("--json", "Output as JSON").option("--quiet", "One-line output for scripts/hooks").option("--agent <type>", "Target agents (comma-separated): claude, cursor, codex", parseAgentOption).action(scoreCommand);
@@ -6969,22 +7032,22 @@ learn.command("remove").description("Remove learning hooks from .claude/settings
 learn.command("status").description("Show learning system status").action(learnStatusCommand);
 
 // src/utils/version-check.ts
-import fs27 from "fs";
+import fs28 from "fs";
 import path23 from "path";
 import { fileURLToPath as fileURLToPath2 } from "url";
 import { execSync as execSync9 } from "child_process";
 import chalk15 from "chalk";
 import ora7 from "ora";
-import confirm2 from "@inquirer/confirm";
+import confirm from "@inquirer/confirm";
 var __dirname_vc = path23.dirname(fileURLToPath2(import.meta.url));
 var pkg2 = JSON.parse(
-  fs27.readFileSync(path23.resolve(__dirname_vc, "..", "package.json"), "utf-8")
+  fs28.readFileSync(path23.resolve(__dirname_vc, "..", "package.json"), "utf-8")
 );
 function getInstalledVersion() {
   try {
     const globalRoot = execSync9("npm root -g", { encoding: "utf-8", stdio: ["pipe", "pipe", "pipe"] }).trim();
     const pkgPath = path23.join(globalRoot, "@rely-ai", "caliber", "package.json");
-    return JSON.parse(fs27.readFileSync(pkgPath, "utf-8")).version;
+    return JSON.parse(fs28.readFileSync(pkgPath, "utf-8")).version;
   } catch {
     return null;
   }
@@ -7020,7 +7083,7 @@ Run ${chalk15.bold("npm install -g @rely-ai/caliber")} to upgrade.
       chalk15.yellow(`
 Update available: ${current} -> ${latest}`)
     );
-    const shouldUpdate = await confirm2({ message: "Would you like to update now? (Y/n)", default: true });
+    const shouldUpdate = await confirm({ message: "Would you like to update now? (Y/n)", default: true });
     if (!shouldUpdate) {
       console.log();
       return;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@rely-ai/caliber",
-  "version": "1.3.3",
+  "version": "1.4.0",
   "description": "Analyze your codebase and generate optimized AI agent configs (CLAUDE.md, .cursorrules, skills) — no API key needed",
   "type": "module",
   "bin": {