@caliber-ai/cli 0.14.0 → 0.14.1

package/dist/bin.js

@@ -1185,20 +1185,8 @@ function writeClaudeConfig(config) {
   const written = [];
   fs9.writeFileSync("CLAUDE.md", config.claudeMd);
   written.push("CLAUDE.md");
-  const claudeDir = ".claude";
-  if (!fs9.existsSync(claudeDir)) fs9.mkdirSync(claudeDir, { recursive: true });
-  fs9.writeFileSync(
-    path10.join(claudeDir, "settings.json"),
-    JSON.stringify(config.settings, null, 2)
-  );
-  written.push(path10.join(claudeDir, "settings.json"));
-  fs9.writeFileSync(
-    path10.join(claudeDir, "settings.local.json"),
-    JSON.stringify(config.settingsLocal, null, 2)
-  );
-  written.push(path10.join(claudeDir, "settings.local.json"));
   if (config.skills?.length) {
-    const skillsDir = path10.join(claudeDir, "skills");
+    const skillsDir = path10.join(".claude", "skills");
     if (!fs9.existsSync(skillsDir)) fs9.mkdirSync(skillsDir, { recursive: true });
     for (const skill of config.skills) {
       const filename = `${skill.name.replace(/[^a-z0-9-]/gi, "-").toLowerCase()}.md`;
@@ -1212,9 +1200,7 @@ function writeClaudeConfig(config) {
     try {
       if (fs9.existsSync(".mcp.json")) {
         const existing = JSON.parse(fs9.readFileSync(".mcp.json", "utf-8"));
-        if (existing.mcpServers) {
-          existingServers = existing.mcpServers;
-        }
+        if (existing.mcpServers) existingServers = existing.mcpServers;
       }
     } catch {
     }
@@ -1319,7 +1305,11 @@ function fileChecksum(filePath) {
 // src/writers/index.ts
 function writeSetup(setup) {
   const filesToWrite = getFilesToWrite(setup);
-  const existingFiles = filesToWrite.filter((f) => fs13.existsSync(f));
+  const filesToDelete = (setup.deletions || []).map((d) => d.filePath).filter((f) => fs13.existsSync(f));
+  const existingFiles = [
+    ...filesToWrite.filter((f) => fs13.existsSync(f)),
+    ...filesToDelete
+  ];
   const backupDir = existingFiles.length > 0 ? createBackup(existingFiles) : void 0;
   const written = [];
   if ((setup.targetAgent === "claude" || setup.targetAgent === "both") && setup.claude) {
@@ -1328,15 +1318,28 @@ function writeSetup(setup) {
   if ((setup.targetAgent === "cursor" || setup.targetAgent === "both") && setup.cursor) {
     written.push(...writeCursorConfig(setup.cursor));
   }
+  const deleted = [];
+  for (const filePath of filesToDelete) {
+    fs13.unlinkSync(filePath);
+    deleted.push(filePath);
+  }
   ensureGitignore();
-  const entries = written.map((file) => ({
-    path: file,
-    action: existingFiles.includes(file) ? "modified" : "created",
-    checksum: fileChecksum(file),
-    timestamp: (/* @__PURE__ */ new Date()).toISOString()
-  }));
+  const entries = [
+    ...written.map((file) => ({
+      path: file,
+      action: existingFiles.includes(file) ? "modified" : "created",
+      checksum: fileChecksum(file),
+      timestamp: (/* @__PURE__ */ new Date()).toISOString()
+    })),
+    ...deleted.map((file) => ({
+      path: file,
+      action: "deleted",
+      checksum: "",
+      timestamp: (/* @__PURE__ */ new Date()).toISOString()
+    }))
+  ];
   writeManifest({ version: 1, backupDir, entries });
-  return { written, backupDir };
+  return { written, deleted, backupDir };
 }
 function undoSetup() {
   const manifest = readManifest();
@@ -1351,7 +1354,7 @@ function undoSetup() {
         fs13.unlinkSync(entry.path);
         removed.push(entry.path);
       }
-    } else if (entry.action === "modified" && manifest.backupDir) {
+    } else if ((entry.action === "modified" || entry.action === "deleted") && manifest.backupDir) {
       if (restoreBackup(manifest.backupDir, entry.path)) {
         restored.push(entry.path);
       }
@@ -1366,7 +1369,7 @@ function undoSetup() {
 function getFilesToWrite(setup) {
   const files = [];
   if ((setup.targetAgent === "claude" || setup.targetAgent === "both") && setup.claude) {
-    files.push("CLAUDE.md", ".claude/settings.json", ".claude/settings.local.json");
+    files.push("CLAUDE.md");
     if (setup.claude.mcpServers) files.push(".mcp.json");
     if (setup.claude.skills) {
       for (const s of setup.claude.skills) {
@@ -1582,10 +1585,10 @@ async function initCommand(options) {
   `));
   console.log(chalk3.dim("  Configure your coding agent environment\n"));
   console.log(chalk3.bold("  What is Caliber?\n"));
-  console.log(chalk3.dim("  Caliber analyzes your project and generates optimized configurations"));
-  console.log(chalk3.dim("  for AI coding agents (Claude Code, Cursor). It creates CLAUDE.md,"));
-  console.log(chalk3.dim("  .cursorrules, skills, permissions, and MCP servers tailored to your"));
-  console.log(chalk3.dim("  codebase \u2014 so your AI agent understands your project from day one.\n"));
+  console.log(chalk3.dim("  Caliber audits your AI agent configurations and suggests targeted"));
+  console.log(chalk3.dim("  improvements. It analyzes CLAUDE.md, .cursorrules, skills, and MCP"));
+  console.log(chalk3.dim("  servers against your actual codebase \u2014 keeping what works, fixing"));
+  console.log(chalk3.dim("  what's stale, and adding what's missing.\n"));
   console.log(chalk3.bold("  How it works:\n"));
   console.log(chalk3.dim("  1. Scan      Analyze your code, dependencies, and file structure"));
   console.log(chalk3.dim("  2. Match     Detect existing configs and check for teammate setups"));
@@ -1704,9 +1707,9 @@ async function initCommand(options) {
   if (isEmpty) {
     fingerprint.description = await promptInput("What will you build in this project?");
   }
-  console.log(chalk3.hex("#6366f1").bold("  Step 4/6 \u2014 Planning a better setup\n"));
-  console.log(chalk3.dim("  AI is building CLAUDE.md, permissions, skills, and rules based on"));
-  console.log(chalk3.dim("  your project's stack and conventions.\n"));
+  console.log(chalk3.hex("#6366f1").bold("  Step 4/6 \u2014 Auditing your configs\n"));
+  console.log(chalk3.dim("  AI is auditing your CLAUDE.md, skills, and rules against your"));
+  console.log(chalk3.dim("  project's actual codebase and conventions.\n"));
   console.log(chalk3.dim("  This usually takes 1\u20133 minutes on first run.\n"));
   let generatedSetup = null;
   let rawOutput;
@@ -1795,11 +1798,21 @@ async function initCommand(options) {
   try {
     const result = writeSetup(generatedSetup);
     writeSpinner.succeed("Config files written");
-    trackEvent("setup_applied", { files_written: result.written.length, target_agent: targetAgent });
+    trackEvent("setup_applied", {
+      files_written: result.written.length,
+      files_deleted: result.deleted.length,
+      target_agent: targetAgent
+    });
     console.log(chalk3.bold("\nFiles created/updated:"));
     for (const file of result.written) {
       console.log(`  ${chalk3.green("\u2713")} ${file}`);
     }
+    if (result.deleted.length > 0) {
+      console.log(chalk3.bold("\nFiles removed:"));
+      for (const file of result.deleted) {
+        console.log(`  ${chalk3.red("\u2717")} ${file}`);
+      }
+    }
     if (result.backupDir) {
       console.log(chalk3.dim(`
   Backups saved to ${result.backupDir}`));
@@ -1936,39 +1949,20 @@ async function promptAction() {
 function printSetupSummary(setup) {
   const claude = setup.claude;
   const cursor = setup.cursor;
+  const fileDescriptions = setup.fileDescriptions;
+  const deletions = setup.deletions;
   console.log("");
-  console.log(chalk3.bold("  Files to create:\n"));
+  console.log(chalk3.bold("  Proposed changes:\n"));
+  const getDescription = (filePath) => {
+    return fileDescriptions?.[filePath];
+  };
   if (claude) {
     if (claude.claudeMd) {
       const icon = fs16.existsSync("CLAUDE.md") ? chalk3.yellow("~") : chalk3.green("+");
-      const sections = extractClaudeMdSections(claude.claudeMd);
+      const desc = getDescription("CLAUDE.md");
       console.log(`  ${icon} ${chalk3.bold("CLAUDE.md")}`);
-      console.log(chalk3.dim("    Your project's knowledge base for the AI agent \u2014 architecture, build"));
-      console.log(chalk3.dim("    commands, conventions. Claude reads this at the start of every session."));
-      if (sections.length > 0) {
-        console.log(chalk3.dim(`    Sections: ${sections.join(", ")}`));
-      }
-      console.log("");
-    }
-    if (claude.settings) {
-      const icon = fs16.existsSync(".claude/settings.json") ? chalk3.yellow("~") : chalk3.green("+");
-      const settings = claude.settings;
-      const perms = settings.permissions?.allow || [];
-      console.log(`  ${icon} ${chalk3.bold(".claude/settings.json")}`);
-      console.log(chalk3.dim("    Pre-approved shell commands so Claude doesn't ask permission each time."));
-      if (perms.length > 0) {
-        console.log(chalk3.dim(`    Allows: ${summarizePermissions(perms)}`));
-      }
-      console.log("");
-    }
-    if (claude.settingsLocal) {
-      const icon = fs16.existsSync(".claude/settings.local.json") ? chalk3.yellow("~") : chalk3.green("+");
-      const settings = claude.settingsLocal;
-      const perms = settings.permissions?.allow || [];
-      console.log(`  ${icon} ${chalk3.bold(".claude/settings.local.json")}`);
-      console.log(chalk3.dim("    Your personal permission overrides (not shared with teammates)."));
-      if (perms.length > 0) {
-        console.log(chalk3.dim(`    Allows: ${summarizePermissions(perms)}`));
+      if (desc) {
+        console.log(chalk3.dim(`    ${desc}`));
       }
       console.log("");
     }
@@ -1977,8 +1971,9 @@ function printSetupSummary(setup) {
       for (const skill of skills) {
         const skillPath = `.claude/skills/${skill.name.replace(/[^a-z0-9-]/gi, "-").toLowerCase()}.md`;
         const icon = fs16.existsSync(skillPath) ? chalk3.yellow("~") : chalk3.green("+");
+        const desc = getDescription(skillPath);
         console.log(`  ${icon} ${chalk3.bold(skillPath)}`);
-        console.log(chalk3.dim(`    ${summarizeSkill(skill)}`));
+        console.log(chalk3.dim(`    ${desc || summarizeSkill(skill)}`));
         console.log("");
       }
     }
@@ -1986,18 +1981,18 @@ function printSetupSummary(setup) {
     if (mcpServers && Object.keys(mcpServers).length > 0) {
       const icon = fs16.existsSync(".mcp.json") ? chalk3.yellow("~") : chalk3.green("+");
       const serverNames = Object.keys(mcpServers);
+      const desc = getDescription(".mcp.json");
       console.log(`  ${icon} ${chalk3.bold(".mcp.json")}`);
-      console.log(chalk3.dim("    Connects Claude to external tools it can call directly."));
-      console.log(chalk3.dim(`    Servers: ${serverNames.join(", ")}`));
+      console.log(chalk3.dim(`    ${desc || `servers: ${serverNames.join(", ")}`}`));
       console.log("");
     }
   }
   if (cursor) {
     if (cursor.cursorrules) {
       const icon = fs16.existsSync(".cursorrules") ? chalk3.yellow("~") : chalk3.green("+");
+      const desc = getDescription(".cursorrules");
       console.log(`  ${icon} ${chalk3.bold(".cursorrules")}`);
-      console.log(chalk3.dim("    Project-wide instructions for Cursor \u2014 coding style, architecture,"));
-      console.log(chalk3.dim("    and conventions. Cursor reads this at the start of every session."));
+      if (desc) console.log(chalk3.dim(`    ${desc}`));
       console.log("");
     }
     const rules = cursor.rules;
@@ -2005,9 +2000,14 @@ function printSetupSummary(setup) {
       for (const rule of rules) {
         const rulePath = `.cursor/rules/${rule.filename}`;
         const icon = fs16.existsSync(rulePath) ? chalk3.yellow("~") : chalk3.green("+");
+        const desc = getDescription(rulePath);
         console.log(`  ${icon} ${chalk3.bold(rulePath)}`);
-        const firstLine = rule.content.split("\n").filter((l) => l.trim() && !l.trim().startsWith("#"))[0];
-        if (firstLine) console.log(chalk3.dim(`    ${firstLine.trim().slice(0, 80)}`));
+        if (desc) {
+          console.log(chalk3.dim(`    ${desc}`));
+        } else {
+          const firstLine = rule.content.split("\n").filter((l) => l.trim() && !l.trim().startsWith("#"))[0];
+          if (firstLine) console.log(chalk3.dim(`    ${firstLine.trim().slice(0, 80)}`));
+        }
         console.log("");
       }
     }
@@ -2015,24 +2015,22 @@ function printSetupSummary(setup) {
     if (mcpServers && Object.keys(mcpServers).length > 0) {
       const icon = fs16.existsSync(".cursor/mcp.json") ? chalk3.yellow("~") : chalk3.green("+");
       const serverNames = Object.keys(mcpServers);
+      const desc = getDescription(".cursor/mcp.json");
       console.log(`  ${icon} ${chalk3.bold(".cursor/mcp.json")}`);
-      console.log(chalk3.dim("    Connects Cursor to external tools it can call directly."));
-      console.log(chalk3.dim(`    Servers: ${serverNames.join(", ")}`));
+      console.log(chalk3.dim(`    ${desc || `servers: ${serverNames.join(", ")}`}`));
+      console.log("");
+    }
+  }
+  if (Array.isArray(deletions) && deletions.length > 0) {
+    for (const del of deletions) {
+      console.log(`  ${chalk3.red("-")} ${chalk3.bold(del.filePath)}`);
+      console.log(chalk3.dim(`    ${del.reason}`));
       console.log("");
     }
   }
-  console.log(`  ${chalk3.green("+")} ${chalk3.dim("new")}  ${chalk3.yellow("~")} ${chalk3.dim("modified")}`);
+  console.log(`  ${chalk3.green("+")} ${chalk3.dim("new")}  ${chalk3.yellow("~")} ${chalk3.dim("modified")}  ${chalk3.red("-")} ${chalk3.dim("removed")}`);
   console.log("");
 }
-function extractClaudeMdSections(md) {
-  return md.split("\n").filter((line) => /^##\s+/.test(line)).map((line) => line.replace(/^##\s+/, "").trim());
-}
-function summarizePermissions(permissions, maxShow = 3) {
-  if (permissions.length === 0) return "None";
-  const shown = permissions.slice(0, maxShow).join(", ");
-  const remaining = permissions.length - maxShow;
-  return remaining > 0 ? `${shown} (+${remaining} more)` : shown;
-}
 function summarizeSkill(skill) {
   const lines = skill.content.split("\n").filter((l) => l.trim() && !l.trim().startsWith("#"));
   return lines[0]?.trim().slice(0, 80) || skill.name;
@@ -2043,8 +2041,6 @@ function collectSetupFiles(setup) {
   const cursor = setup.cursor;
   if (claude) {
     if (claude.claudeMd) files.push({ path: "CLAUDE.md", content: claude.claudeMd });
-    if (claude.settings) files.push({ path: ".claude/settings.json", content: JSON.stringify(claude.settings, null, 2) });
-    if (claude.settingsLocal) files.push({ path: ".claude/settings.local.json", content: JSON.stringify(claude.settingsLocal, null, 2) });
     const skills = claude.skills;
     if (Array.isArray(skills)) {
       for (const skill of skills) {