@rely-ai/caliber 1.37.0 → 1.38.0

package/dist/bin.js

@@ -1099,14 +1099,14 @@ __export(lock_exports, {
   isCaliberRunning: () => isCaliberRunning,
   releaseLock: () => releaseLock
 });
-import fs39 from "fs";
-import path32 from "path";
+import fs40 from "fs";
+import path33 from "path";
 import os8 from "os";
 import crypto5 from "crypto";
 function buildLockPath() {
   const cwd = process.cwd();
   const hash = crypto5.createHash("md5").update(cwd).digest("hex").slice(0, 8);
-  return path32.join(os8.tmpdir(), `.caliber-${hash}.lock`);
+  return path33.join(os8.tmpdir(), `.caliber-${hash}.lock`);
 }
 function getLockFile() {
   if (!_lockPath) _lockPath = buildLockPath();
@@ -1115,8 +1115,8 @@ function getLockFile() {
 function isCaliberRunning() {
   try {
     const lockFile = buildLockPath();
-    if (!fs39.existsSync(lockFile)) return false;
-    const raw = fs39.readFileSync(lockFile, "utf-8").trim();
+    if (!fs40.existsSync(lockFile)) return false;
+    const raw = fs40.readFileSync(lockFile, "utf-8").trim();
     const { pid, ts } = JSON.parse(raw);
     if (Date.now() - ts > STALE_MS) return false;
     try {
@@ -1131,14 +1131,14 @@ function isCaliberRunning() {
 }
 function acquireLock() {
   try {
-    fs39.writeFileSync(getLockFile(), JSON.stringify({ pid: process.pid, ts: Date.now() }));
+    fs40.writeFileSync(getLockFile(), JSON.stringify({ pid: process.pid, ts: Date.now() }));
   } catch {
   }
 }
 function releaseLock() {
   try {
     const lockFile = getLockFile();
-    if (fs39.existsSync(lockFile)) fs39.unlinkSync(lockFile);
+    if (fs40.existsSync(lockFile)) fs40.unlinkSync(lockFile);
   } catch {
   }
 }
@@ -1153,8 +1153,8 @@ var init_lock = __esm({
 
 // src/cli.ts
 import { Command } from "commander";
-import fs50 from "fs";
-import path41 from "path";
+import fs51 from "fs";
+import path42 from "path";
 import { fileURLToPath } from "url";
 
 // src/commands/init.ts
@@ -2352,6 +2352,55 @@ function isRateLimitError(stderr) {
   return /rate limit|too many requests|429/i.test(stderr);
 }
 
+// src/llm/utils.ts
+function extractJson(text) {
+  const startIdx = text.search(/[[{]/);
+  if (startIdx === -1) return null;
+  let depth = 0;
+  let inString = false;
+  let escaped = false;
+  for (let i = startIdx; i < text.length; i++) {
+    const ch = text[i];
+    if (escaped) {
+      escaped = false;
+      continue;
+    }
+    if (ch === "\\" && inString) {
+      escaped = true;
+      continue;
+    }
+    if (ch === '"') {
+      inString = !inString;
+      continue;
+    }
+    if (inString) continue;
+    if (ch === "{" || ch === "[") depth++;
+    if (ch === "}" || ch === "]") {
+      depth--;
+      if (depth === 0) return text.slice(startIdx, i + 1);
+    }
+  }
+  return null;
+}
+function stripMarkdownFences(text) {
+  return text.replace(/^```(?:json)?\s*/im, "").replace(/```\s*$/m, "").trim();
+}
+function parseJsonResponse(raw) {
+  const cleaned = stripMarkdownFences(raw);
+  try {
+    return JSON.parse(cleaned);
+  } catch {
+  }
+  const json = extractJson(cleaned);
+  if (!json) {
+    throw new Error(`No JSON found in LLM response: ${raw.slice(0, 200)}`);
+  }
+  return JSON.parse(json);
+}
+function estimateTokens(text) {
+  return Math.ceil(text.length / 4);
+}
+
 // src/llm/cursor-acp.ts
 var AGENT_BIN = "agent";
 var IS_WINDOWS = process.platform === "win32";
@@ -2376,12 +2425,33 @@ var CursorAcpProvider = class {
   async call(options) {
     const prompt = this.buildPrompt(options);
     const model = options.model || this.defaultModel;
-    return this.runPrint(model, prompt);
+    const result = await this.runPrint(model, prompt);
+    trackUsage(model, {
+      inputTokens: estimateTokens(prompt),
+      outputTokens: estimateTokens(result)
+    });
+    return result;
   }
   async stream(options, callbacks) {
     const prompt = this.buildPrompt(options);
     const model = options.model || this.defaultModel;
-    return this.runPrintStream(model, prompt, callbacks);
+    const inputEstimate = estimateTokens(prompt);
+    let outputChars = 0;
+    const wrappedCallbacks = {
+      onText: (text) => {
+        outputChars += text.length;
+        callbacks.onText(text);
+      },
+      onEnd: (meta) => {
+        trackUsage(model, {
+          inputTokens: inputEstimate,
+          outputTokens: Math.ceil(outputChars / 4)
+        });
+        callbacks.onEnd(meta);
+      },
+      onError: (err) => callbacks.onError(err)
+    };
+    return this.runPrintStream(model, prompt, wrappedCallbacks);
   }
   /**
    * Pre-spawn an agent process so it's ready when the first call comes.
@@ -2473,7 +2543,11 @@ var CursorAcpProvider = class {
         this.killWithEscalation(child);
         if (!settled) {
           settled = true;
-          reject(new Error(`Cursor agent timed out after ${this.timeoutMs / 1e3}s. Set CALIBER_CURSOR_TIMEOUT_MS to increase.`));
+          reject(
+            new Error(
+              `Cursor agent timed out after ${this.timeoutMs / 1e3}s. Set CALIBER_CURSOR_TIMEOUT_MS to increase.`
+            )
+          );
         }
       }, this.timeoutMs);
       timer.unref();
@@ -2509,7 +2583,9 @@ var CursorAcpProvider = class {
         this.killWithEscalation(child);
         if (!settled) {
           settled = true;
-          const err = new Error(`Cursor agent timed out after ${this.timeoutMs / 1e3}s. Set CALIBER_CURSOR_TIMEOUT_MS to increase.`);
+          const err = new Error(
+            `Cursor agent timed out after ${this.timeoutMs / 1e3}s. Set CALIBER_CURSOR_TIMEOUT_MS to increase.`
+          );
           callbacks.onError(err);
           reject(err);
         }
@@ -2616,7 +2692,10 @@ function isCursorAgentAvailable() {
 }
 function isCursorLoggedIn() {
   try {
-    const result = execSync5(`${AGENT_BIN} status`, { stdio: ["ignore", "pipe", "ignore"], timeout: 5e3 });
+    const result = execSync5(`${AGENT_BIN} status`, {
+      stdio: ["ignore", "pipe", "ignore"],
+      timeout: 5e3
+    });
     return !result.toString().includes("not logged in");
   } catch {
     return false;
@@ -2653,20 +2732,29 @@ var ClaudeCliProvider = class {
   }
   async call(options) {
     const combined = this.buildCombinedPrompt(options);
-    return this.runClaudePrint(combined, options.model);
+    const result = await this.runClaudePrint(combined, options.model);
+    trackUsage(options.model || this.defaultModel, {
+      inputTokens: estimateTokens(combined),
+      outputTokens: estimateTokens(result)
+    });
+    return result;
   }
   async stream(options, callbacks) {
     const combined = this.buildCombinedPrompt(options);
+    const inputEstimate = estimateTokens(combined);
     const args = ["-p"];
     if (options.model) args.push("--model", options.model);
     const child = spawnClaude(args);
     child.stdin.end(combined);
     let settled = false;
+    let outputChars = 0;
     const chunks = [];
     const stderrChunks = [];
     child.stdout.on("data", (chunk) => {
       chunks.push(chunk);
-      callbacks.onText(chunk.toString("utf-8"));
+      const text = chunk.toString("utf-8");
+      outputChars += text.length;
+      callbacks.onText(text);
     });
     child.stderr.on("data", (chunk) => stderrChunks.push(chunk));
     const timer = setTimeout(() => {
@@ -2692,6 +2780,11 @@ var ClaudeCliProvider = class {
       if (settled) return;
       settled = true;
       if (code === 0) {
+        const model = options.model || this.defaultModel;
+        trackUsage(model, {
+          inputTokens: inputEstimate,
+          outputTokens: Math.ceil(outputChars / 4)
+        });
         callbacks.onEnd({ stopReason: "end_turn" });
       } else {
         const stderr = Buffer.concat(stderrChunks).toString("utf-8").trim();
@@ -2766,55 +2859,6 @@ function isClaudeCliAvailable() {
   }
 }
 
-// src/llm/utils.ts
-function extractJson(text) {
-  const startIdx = text.search(/[[{]/);
-  if (startIdx === -1) return null;
-  let depth = 0;
-  let inString = false;
-  let escaped = false;
-  for (let i = startIdx; i < text.length; i++) {
-    const ch = text[i];
-    if (escaped) {
-      escaped = false;
-      continue;
-    }
-    if (ch === "\\" && inString) {
-      escaped = true;
-      continue;
-    }
-    if (ch === '"') {
-      inString = !inString;
-      continue;
-    }
-    if (inString) continue;
-    if (ch === "{" || ch === "[") depth++;
-    if (ch === "}" || ch === "]") {
-      depth--;
-      if (depth === 0) return text.slice(startIdx, i + 1);
-    }
-  }
-  return null;
-}
-function stripMarkdownFences(text) {
-  return text.replace(/^```(?:json)?\s*/im, "").replace(/```\s*$/m, "").trim();
-}
-function parseJsonResponse(raw) {
-  const cleaned = stripMarkdownFences(raw);
-  try {
-    return JSON.parse(cleaned);
-  } catch {
-  }
-  const json = extractJson(cleaned);
-  if (!json) {
-    throw new Error(`No JSON found in LLM response: ${raw.slice(0, 200)}`);
-  }
-  return JSON.parse(json);
-}
-function estimateTokens(text) {
-  return Math.ceil(text.length / 4);
-}
-
 // src/llm/model-recovery.ts
 init_config();
 init_resolve_caliber();
@@ -3651,7 +3695,7 @@ function getDetectedWorkspaces(dir) {
 
 // src/fingerprint/index.ts
 async function collectFingerprint(dir) {
-  const gitRemoteUrl = getGitRemoteUrl();
+  const gitRemoteUrl = getGitRemoteUrl(dir);
   const fileTree = getFileTree(dir);
   const existingConfigs = readExistingConfigs(dir);
   const packageName = readPackageName(dir);
@@ -4654,15 +4698,15 @@ init_config();
 // src/utils/dependencies.ts
 import { readFileSync as readFileSync2 } from "fs";
 import { join as join2 } from "path";
-function readFileOrNull2(path43) {
+function readFileOrNull2(path44) {
   try {
-    return readFileSync2(path43, "utf-8");
+    return readFileSync2(path44, "utf-8");
   } catch {
     return null;
   }
 }
-function readJsonOrNull(path43) {
-  const content = readFileOrNull2(path43);
+function readJsonOrNull(path44) {
+  const content = readFileOrNull2(path44);
   if (!content) return null;
   try {
     return JSON.parse(content);
@@ -4761,9 +4805,25 @@ function isTransientError2(error) {
 async function generateSetup(fingerprint, targetAgent, prompt, callbacks, failingChecks, currentScore, passingChecks, options) {
   const isTargetedFix = failingChecks && failingChecks.length > 0 && currentScore !== void 0 && currentScore >= 95 || options?.forceTargetedFix;
   if (isTargetedFix) {
-    return generateMonolithic(fingerprint, targetAgent, prompt, callbacks, failingChecks, currentScore, passingChecks);
+    return generateMonolithic(
+      fingerprint,
+      targetAgent,
+      prompt,
+      callbacks,
+      failingChecks,
+      currentScore,
+      passingChecks
+    );
   }
-  const coreResult = await generateCore(fingerprint, targetAgent, prompt, callbacks, failingChecks, currentScore, passingChecks);
+  const coreResult = await generateCore(
+    fingerprint,
+    targetAgent,
+    prompt,
+    callbacks,
+    failingChecks,
+    currentScore,
+    passingChecks
+  );
   if (!coreResult.setup) {
     return coreResult;
   }
@@ -4812,6 +4872,7 @@ function mergeSkillResults(results, setup) {
   }
   return { succeeded, failed };
 }
+var MAX_SKILL_TOPICS = 5;
 function collectSkillTopics(setup, targetAgent, fingerprint) {
   const topics = [];
   for (const platform of ["claude", "codex", "opencode", "cursor"]) {
@@ -4832,12 +4893,18 @@ function collectSkillTopics(setup, targetAgent, fingerprint) {
       delete platformObj.skillTopics;
     }
   }
-  return topics;
+  return topics.slice(0, MAX_SKILL_TOPICS);
 }
 function getDefaultSkillTopics(fingerprint) {
   const topics = [
-    { name: "development-workflow", description: "Development setup and common workflows. Use when starting development, running the project, or setting up the environment." },
-    { name: "testing-guide", description: "Testing patterns and commands. Use when writing tests, running test suites, or debugging test failures." }
+    {
+      name: "development-workflow",
+      description: "Development setup and common workflows. Use when starting development, running the project, or setting up the environment."
+    },
+    {
+      name: "testing-guide",
+      description: "Testing patterns and commands. Use when writing tests, running test suites, or debugging test failures."
+    }
   ];
   if (fingerprint.frameworks.length > 0) {
     topics.push({
@@ -4855,8 +4922,10 @@ function getDefaultSkillTopics(fingerprint) {
 function buildSkillContext(fingerprint, setup, allDeps) {
   const parts = [];
   if (fingerprint.packageName) parts.push(`Project: ${fingerprint.packageName}`);
-  if (fingerprint.languages.length > 0) parts.push(`Languages: ${fingerprint.languages.join(", ")}`);
-  if (fingerprint.frameworks.length > 0) parts.push(`Frameworks: ${fingerprint.frameworks.join(", ")}`);
+  if (fingerprint.languages.length > 0)
+    parts.push(`Languages: ${fingerprint.languages.join(", ")}`);
+  if (fingerprint.frameworks.length > 0)
+    parts.push(`Frameworks: ${fingerprint.frameworks.join(", ")}`);
   const claude = setup.claude;
   const claudeMd = claude?.claudeMd;
   if (claudeMd) {
@@ -4943,7 +5012,9 @@ async function streamGeneration(config) {
                 }
               }
               sentStatuses = completedLines.length;
-              const jsonStartMatch = preJsonBuffer.match(/(?:^|\n)\s*(?:```json\s*\n\s*)?\{(?=\s*")/);
+              const jsonStartMatch = preJsonBuffer.match(
+                /(?:^|\n)\s*(?:```json\s*\n\s*)?\{(?=\s*")/
+              );
               if (jsonStartMatch) {
                 const matchIndex = preJsonBuffer.indexOf("{", jsonStartMatch.index);
                 inJson = true;
@@ -4958,7 +5029,9 @@ async function streamGeneration(config) {
             let setup = null;
             let jsonToParse = (jsonContent || preJsonBuffer).replace(/```\s*$/g, "").trim();
             if (!jsonContent && preJsonBuffer) {
-              const fallbackMatch = preJsonBuffer.match(/(?:^|\n)\s*(?:```json\s*\n\s*)?\{(?=\s*")/);
+              const fallbackMatch = preJsonBuffer.match(
+                /(?:^|\n)\s*(?:```json\s*\n\s*)?\{(?=\s*")/
+              );
               if (fallbackMatch) {
                 const matchIndex = preJsonBuffer.indexOf("{", fallbackMatch.index);
                 jsonToParse = preJsonBuffer.slice(matchIndex).replace(/```\s*$/g, "").trim();
@@ -4969,7 +5042,10 @@ async function streamGeneration(config) {
             } catch {
             }
             if (!setup && stopReason === "max_tokens" && attempt < MAX_RETRIES2) {
-              if (config.callbacks) config.callbacks.onStatus("Output was truncated, retrying with higher token limit...");
+              if (config.callbacks)
+                config.callbacks.onStatus(
+                  "Output was truncated, retrying with higher token limit..."
+                );
               setTimeout(() => attemptGeneration().then(resolve3), 1e3);
               return;
             }
@@ -4982,12 +5058,18 @@ async function streamGeneration(config) {
               if (config.callbacks) config.callbacks.onComplete(setup, explanation);
               resolve3({ setup, explanation, stopReason: stopReason ?? void 0 });
             } else {
-              resolve3({ setup: null, explanation, raw: preJsonBuffer, stopReason: stopReason ?? void 0 });
+              resolve3({
+                setup: null,
+                explanation,
+                raw: preJsonBuffer,
+                stopReason: stopReason ?? void 0
+              });
             }
           },
           onError: (error) => {
             if (isTransientError2(error) && attempt < MAX_RETRIES2) {
-              if (config.callbacks) config.callbacks.onStatus("Connection interrupted, retrying...");
+              if (config.callbacks)
+                config.callbacks.onStatus("Connection interrupted, retrying...");
               setTimeout(() => attemptGeneration().then(resolve3), 2e3);
               return;
             }
@@ -5004,7 +5086,14 @@ async function streamGeneration(config) {
   return attemptGeneration();
 }
 async function generateCore(fingerprint, targetAgent, prompt, callbacks, failingChecks, currentScore, passingChecks) {
-  const userMessage = buildGeneratePrompt(fingerprint, targetAgent, prompt, failingChecks, currentScore, passingChecks);
+  const userMessage = buildGeneratePrompt(
+    fingerprint,
+    targetAgent,
+    prompt,
+    failingChecks,
+    currentScore,
+    passingChecks
+  );
   return streamGeneration({
     systemPrompt: CORE_GENERATION_PROMPT,
     userMessage,
@@ -5015,7 +5104,14 @@ async function generateCore(fingerprint, targetAgent, prompt, callbacks, failing
   });
 }
 async function generateMonolithic(fingerprint, targetAgent, prompt, callbacks, failingChecks, currentScore, passingChecks) {
-  const userMessage = buildGeneratePrompt(fingerprint, targetAgent, prompt, failingChecks, currentScore, passingChecks);
+  const userMessage = buildGeneratePrompt(
+    fingerprint,
+    targetAgent,
+    prompt,
+    failingChecks,
+    currentScore,
+    passingChecks
+  );
   return streamGeneration({
     systemPrompt: GENERATION_SYSTEM_PROMPT,
     userMessage,
@@ -5096,9 +5192,11 @@ function buildGeneratePrompt(fingerprint, targetAgent, prompt, failingChecks, cu
   const isTargetedFix = failingChecks && failingChecks.length > 0 && currentScore !== void 0 && currentScore >= 95;
   if (isTargetedFix) {
     parts.push(`TARGETED FIX MODE \u2014 current score: ${currentScore}/100, target: ${targetAgent}`);
-    parts.push(`
+    parts.push(
+      `
 The existing config is already high quality. ONLY fix these specific failing checks:
-`);
+`
+    );
     for (const check of failingChecks) {
       if (check.fix) {
         parts.push(`- **${check.name}**`);
@@ -5129,15 +5227,19 @@ IMPORTANT RULES FOR TARGETED FIX:
 - For grounding issues: Add references to the listed project directories in the appropriate sections.
 - Every path or name you reference MUST exist in the project \u2014 use the file tree provided below.`);
   } else if (hasExistingConfigs) {
-    parts.push(`Audit and improve the existing coding agent configuration for target: ${targetAgent}`);
+    parts.push(
+      `Audit and improve the existing coding agent configuration for target: ${targetAgent}`
+    );
   } else {
     parts.push(`Generate an initial coding agent configuration for target: ${targetAgent}`);
   }
   if (fingerprint.gitRemoteUrl) parts.push(`
 Git remote: ${fingerprint.gitRemoteUrl}`);
   if (fingerprint.packageName) parts.push(`Package name: ${fingerprint.packageName}`);
-  if (fingerprint.languages.length > 0) parts.push(`Languages: ${fingerprint.languages.join(", ")}`);
-  if (fingerprint.frameworks.length > 0) parts.push(`Frameworks: ${fingerprint.frameworks.join(", ")}`);
+  if (fingerprint.languages.length > 0)
+    parts.push(`Languages: ${fingerprint.languages.join(", ")}`);
+  if (fingerprint.frameworks.length > 0)
+    parts.push(`Frameworks: ${fingerprint.frameworks.join(", ")}`);
   if (fingerprint.description) parts.push(`Project description: ${fingerprint.description}`);
   if (fingerprint.fileTree.length > 0) {
     const caPaths = fingerprint.codeAnalysis?.files.map((f) => f.path) ?? [];
@@ -5146,36 +5248,52 @@ Git remote: ${fingerprint.gitRemoteUrl}`);
 File tree (${tree.length}/${fingerprint.fileTree.length}):
 ${tree.join("\n")}`);
   }
-  if (existing.claudeMd) parts.push(`
+  if (existing.claudeMd)
+    parts.push(
+      `
 Existing CLAUDE.md:
-${truncate(existing.claudeMd, LIMITS.EXISTING_CONFIG_CHARS)}`);
-  if (existing.agentsMd) parts.push(`
+${truncate(existing.claudeMd, LIMITS.EXISTING_CONFIG_CHARS)}`
+    );
+  if (existing.agentsMd)
+    parts.push(
+      `
 Existing AGENTS.md:
-${truncate(existing.agentsMd, LIMITS.EXISTING_CONFIG_CHARS)}`);
-  if (existing.readmeMd) parts.push(`
+${truncate(existing.agentsMd, LIMITS.EXISTING_CONFIG_CHARS)}`
+    );
+  if (existing.readmeMd)
+    parts.push(
+      `
 Existing README.md:
-${truncate(existing.readmeMd, LIMITS.EXISTING_CONFIG_CHARS)}`);
+${truncate(existing.readmeMd, LIMITS.EXISTING_CONFIG_CHARS)}`
+    );
   if (existing.claudeSkills?.length) {
     parts.push("\n--- Existing Claude Skills ---");
     for (const skill of existing.claudeSkills.slice(0, LIMITS.SKILLS_MAX)) {
-      parts.push(`
+      parts.push(
+        `
 [.claude/skills/${skill.filename}]
-${truncate(skill.content, LIMITS.SKILL_CHARS)}`);
+${truncate(skill.content, LIMITS.SKILL_CHARS)}`
+      );
     }
     if (existing.claudeSkills.length > LIMITS.SKILLS_MAX) {
       parts.push(`
 (${existing.claudeSkills.length - LIMITS.SKILLS_MAX} more skills omitted)`);
     }
   }
-  if (existing.cursorrules) parts.push(`
+  if (existing.cursorrules)
+    parts.push(
+      `
 Existing .cursorrules:
-${truncate(existing.cursorrules, LIMITS.EXISTING_CONFIG_CHARS)}`);
+${truncate(existing.cursorrules, LIMITS.EXISTING_CONFIG_CHARS)}`
+    );
   if (existing.cursorRules?.length) {
     parts.push("\n--- Existing Cursor Rules ---");
     for (const rule of existing.cursorRules.slice(0, LIMITS.RULES_MAX)) {
-      parts.push(`
+      parts.push(
+        `
 [.cursor/rules/${rule.filename}]
-${truncate(rule.content, LIMITS.SKILL_CHARS)}`);
+${truncate(rule.content, LIMITS.SKILL_CHARS)}`
+      );
     }
     if (existing.cursorRules.length > LIMITS.RULES_MAX) {
       parts.push(`
@@ -5185,9 +5303,11 @@ ${truncate(rule.content, LIMITS.SKILL_CHARS)}`);
   if (existing.cursorSkills?.length) {
     parts.push("\n--- Existing Cursor Skills ---");
     for (const skill of existing.cursorSkills.slice(0, LIMITS.SKILLS_MAX)) {
-      parts.push(`
+      parts.push(
+        `
 [.cursor/skills/${skill.name}/SKILL.md]
-${truncate(skill.content, LIMITS.SKILL_CHARS)}`);
+${truncate(skill.content, LIMITS.SKILL_CHARS)}`
+      );
     }
     if (existing.cursorSkills.length > LIMITS.SKILLS_MAX) {
       parts.push(`
@@ -5195,9 +5315,11 @@ ${truncate(skill.content, LIMITS.SKILL_CHARS)}`);
     }
   }
   if (existing.personalLearnings) {
-    parts.push(`
+    parts.push(
+      `
 --- Personal Learnings (developer-specific, include in generated configs) ---
-${existing.personalLearnings}`);
+${existing.personalLearnings}`
+    );
   }
   const allDeps = extractAllDeps(process.cwd());
   if (allDeps.length > 0) {
@@ -5263,7 +5385,10 @@ import fs12 from "fs";
 import path12 from "path";
 function writeClaudeConfig(config) {
   const written = [];
-  fs12.writeFileSync("CLAUDE.md", appendSyncBlock(appendLearningsBlock(appendPreCommitBlock(config.claudeMd))));
+  fs12.writeFileSync(
+    "CLAUDE.md",
+    appendSyncBlock(appendLearningsBlock(appendPreCommitBlock(config.claudeMd)))
+  );
   written.push("CLAUDE.md");
   if (config.skills?.length) {
     for (const skill of config.skills) {
@@ -7501,8 +7626,8 @@ function trackInitSkillsSearch(searched, installedCount) {
 function trackInitScoreRegression(oldScore, newScore) {
   trackEvent("init_score_regression", { old_score: oldScore, new_score: newScore });
 }
-function trackInitCompleted(path43, score) {
-  trackEvent("init_completed", { path: path43, score });
+function trackInitCompleted(path44, score) {
+  trackEvent("init_completed", { path: path44, score });
 }
 function trackRegenerateCompleted(action, durationMs) {
   trackEvent("regenerate_completed", { action, duration_ms: durationMs });
@@ -7864,10 +7989,13 @@ async function searchSkills(fingerprint, targetPlatforms, onStatus) {
   if (!newCandidates.length) {
     return { results: [], contentMap: /* @__PURE__ */ new Map() };
   }
-  onStatus?.(`Scoring ${newCandidates.length} candidates...`);
   let results;
   const config = loadConfig();
-  if (config) {
+  if (newCandidates.length <= 5) {
+    onStatus?.("Few candidates \u2014 skipping scoring");
+    results = newCandidates.map((c) => ({ ...c, score: 70 }));
+  } else if (config) {
+    onStatus?.(`Scoring ${newCandidates.length} candidates...`);
     try {
       const projectContext = buildProjectContext(fingerprint, targetPlatforms);
       results = await scoreWithLLM(newCandidates, projectContext, technologies);
@@ -8286,7 +8414,8 @@ function printSkills(recs) {
 // src/ai/score-refine.ts
 import { existsSync as existsSync9 } from "fs";
 import ora2 from "ora";
-var MAX_REFINE_ITERATIONS = 2;
+var MAX_REFINE_ITERATIONS = 1;
+var MIN_POINTS_TO_REFINE = 4;
 function extractConfigContent(setup) {
   const claude = setup.claude;
   const codex = setup.codex;
@@ -8296,7 +8425,11 @@ function extractConfigContent(setup) {
     cursorrules = cursor.cursorrules;
   }
   const skills = [];
-  for (const [platform, obj] of [["claude", claude], ["codex", codex], ["cursor", cursor]]) {
+  for (const [platform, obj] of [
+    ["claude", claude],
+    ["codex", codex],
+    ["cursor", cursor]
+  ]) {
     const platformSkills = obj?.skills;
     if (Array.isArray(platformSkills)) {
       for (const skill of platformSkills) {
@@ -8315,8 +8448,12 @@ function extractConfigContent(setup) {
 }
 function buildGroundingFixInstruction(unmentionedTopDirs, projectStructure) {
   const dirDescriptions = unmentionedTopDirs.slice(0, 8).map((dir) => {
-    const subdirs = projectStructure.dirs.filter((d) => d.startsWith(`${dir}/`) && !d.includes("/", dir.length + 1));
-    const files = projectStructure.files.filter((f) => f.startsWith(`${dir}/`) && !f.includes("/", dir.length + 1));
+    const subdirs = projectStructure.dirs.filter(
+      (d) => d.startsWith(`${dir}/`) && !d.includes("/", dir.length + 1)
+    );
+    const files = projectStructure.files.filter(
+      (f) => f.startsWith(`${dir}/`) && !f.includes("/", dir.length + 1)
+    );
     const children = [...subdirs.slice(0, 4), ...files.slice(0, 2)];
     const childList = children.map((c) => c.split("/").pop()).join(", ");
     return childList ? `- \`${dir}/\` (contains: ${childList})` : `- \`${dir}/\``;
@@ -8361,7 +8498,9 @@ function validateSetup(setup, dir, checkExists = existsSync9, projectStructure)
   const content = claudeMd ?? agentsMd ?? "";
   if (content) {
     const structure2 = analyzeMarkdownStructure(content);
-    const blockThreshold = CODE_BLOCK_THRESHOLDS.find((t) => structure2.codeBlockCount >= t.minBlocks);
+    const blockThreshold = CODE_BLOCK_THRESHOLDS.find(
+      (t) => structure2.codeBlockCount >= t.minBlocks
+    );
     const blockPoints = blockThreshold?.points ?? 0;
     const maxBlockPoints = CODE_BLOCK_THRESHOLDS[0].points;
     if (blockPoints < maxBlockPoints && structure2.codeBlockCount < CODE_BLOCK_THRESHOLDS[0].minBlocks) {
@@ -8486,7 +8625,9 @@ function buildFeedbackMessage(issues) {
   ];
   for (let i = 0; i < issues.length; i++) {
     const issue = issues[i];
-    lines.push(`${i + 1}. ${issue.check.toUpperCase()} (-${issue.pointsLost} pts): ${issue.detail}`);
+    lines.push(
+      `${i + 1}. ${issue.check.toUpperCase()} (-${issue.pointsLost} pts): ${issue.detail}`
+    );
     lines.push(`   Action: ${issue.fixInstruction}
 `);
   }
@@ -8495,20 +8636,22 @@ function buildFeedbackMessage(issues) {
 function countIssuePoints(issues) {
   return issues.reduce((sum, i) => sum + i.pointsLost, 0);
 }
-async function scoreAndRefine(setup, dir, sessionHistory, callbacks) {
+async function scoreAndRefine(setup, dir, sessionHistory, callbacks, options) {
+  const maxIterations = options?.thorough ? 3 : MAX_REFINE_ITERATIONS;
+  const minPoints = options?.thorough ? 1 : MIN_POINTS_TO_REFINE;
   const existsCache = /* @__PURE__ */ new Map();
-  const cachedExists = (path43) => {
-    const cached = existsCache.get(path43);
+  const cachedExists = (path44) => {
+    const cached = existsCache.get(path44);
     if (cached !== void 0) return cached;
-    const result = existsSync9(path43);
-    existsCache.set(path43, result);
+    const result = existsSync9(path44);
+    existsCache.set(path44, result);
     return result;
   };
   const projectStructure = collectProjectStructure(dir);
   let currentSetup = setup;
   let bestSetup = setup;
   let bestLostPoints = Infinity;
-  for (let iteration = 0; iteration < MAX_REFINE_ITERATIONS; iteration++) {
+  for (let iteration = 0; iteration < maxIterations; iteration++) {
     const issues = validateSetup(currentSetup, dir, cachedExists, projectStructure);
     const lostPoints = countIssuePoints(issues);
     if (lostPoints < bestLostPoints) {
@@ -8519,10 +8662,16 @@ async function scoreAndRefine(setup, dir, sessionHistory, callbacks) {
       if (callbacks?.onStatus) callbacks.onStatus("Config passes all scoring checks");
       return bestSetup;
     }
+    if (lostPoints < minPoints) {
+      if (callbacks?.onStatus) callbacks.onStatus("Minor issues \u2014 skipping refinement");
+      return bestSetup;
+    }
     const pointIssues = issues.filter((i) => i.pointsLost > 0);
     const pointIssueNames = pointIssues.map((i) => i.check).join(", ");
     if (callbacks?.onStatus) {
-      callbacks.onStatus(`Fixing ${pointIssues.length} scoring issue${pointIssues.length === 1 ? "" : "s"}: ${pointIssueNames}...`);
+      callbacks.onStatus(
+        `Fixing ${pointIssues.length} scoring issue${pointIssues.length === 1 ? "" : "s"}: ${pointIssueNames}...`
+      );
     }
     const refined = await applyTargetedFixes(currentSetup, issues);
     if (!refined) {
@@ -8557,17 +8706,19 @@ async function applyTargetedFixes(setup, issues) {
   }
   for (const skill of skills) {
     if (failingChecks.has(`Skill quality: ${skill.name}`)) {
-      targets.push({ key: `skill:${skill.name}`, label: `Skill: ${skill.name}`, content: skill.content });
+      targets.push({
+        key: `skill:${skill.name}`,
+        label: `Skill: ${skill.name}`,
+        content: skill.content
+      });
     }
   }
   if (targets.length === 0) return null;
   const feedbackMessage = buildFeedbackMessage(issues);
-  const contentBlock = targets.map(
-    (t) => `### ${t.label}
+  const contentBlock = targets.map((t) => `### ${t.label}
 \`\`\`markdown
 ${t.content}
-\`\`\``
-  ).join("\n\n");
+\`\`\``).join("\n\n");
   const prompt = [
     "Here are the config files with scoring issues:\n",
     contentBlock,
@@ -8618,14 +8769,20 @@ Return ONLY the fixed content as a JSON object with keys ${targets.map((t) => `"
     return null;
   }
 }
-async function runScoreRefineWithSpinner(setup, dir, sessionHistory) {
+async function runScoreRefineWithSpinner(setup, dir, sessionHistory, options) {
   const spinner = ora2("Validating config against scoring criteria...").start();
   try {
-    const refined = await scoreAndRefine(setup, dir, sessionHistory, {
-      onStatus: (msg) => {
-        spinner.text = msg;
-      }
-    });
+    const refined = await scoreAndRefine(
+      setup,
+      dir,
+      sessionHistory,
+      {
+        onStatus: (msg) => {
+          spinner.text = msg;
+        }
+      },
+      options
+    );
     if (refined !== setup) {
       spinner.succeed("Config refined based on scoring feedback");
     } else {
@@ -9365,6 +9522,7 @@ async function refineLoop(currentSetup, sessionHistory, summarizeSetup2, printSu
 // src/commands/init-display.ts
 import chalk12 from "chalk";
 import fs31 from "fs";
+init_types();
 function formatWhatChanged(setup) {
   const lines = [];
   const claude = setup.claude;
@@ -9534,7 +9692,11 @@ function displayTokenUsage() {
     console.log(chalk12.dim("  Token tracking not available for this provider.\n"));
     return;
   }
-  console.log(chalk12.bold("  Token usage:\n"));
+  const config = loadConfig();
+  const isEstimated = config != null && isSeatBased(config.provider);
+  const label = isEstimated ? "Estimated token usage:" : "Token usage:";
+  console.log(chalk12.bold(`  ${label}
+`));
   let totalIn = 0;
   let totalOut = 0;
   for (const m of summary) {
@@ -9552,6 +9714,9 @@ function displayTokenUsage() {
       `    ${chalk12.dim("Total")}: ${totalIn.toLocaleString()} in / ${totalOut.toLocaleString()} out`
     );
   }
+  if (isEstimated) {
+    console.log(chalk12.dim("  (Estimated from character count)"));
+  }
   console.log("");
 }
 
@@ -10233,9 +10398,15 @@ async function initCommand(options) {
         content: summarizeSetup("Initial generation", generatedSetup)
       });
       try {
-        const refined = await scoreAndRefine(generatedSetup, process.cwd(), sessionHistory, {
-          onStatus: (msg) => display.update(TASK_SCORE_REFINE, "running", msg)
-        });
+        const refined = await scoreAndRefine(
+          generatedSetup,
+          process.cwd(),
+          sessionHistory,
+          {
+            onStatus: (msg) => display.update(TASK_SCORE_REFINE, "running", msg)
+          },
+          { thorough: options.thorough }
+        );
         if (refined !== generatedSetup) {
           display.update(TASK_SCORE_REFINE, "done", "Refined");
           generatedSetup = refined;
@@ -10880,8 +11051,8 @@ async function scoreCommand(options) {
 }
 
 // src/commands/refresh.ts
-import fs40 from "fs";
-import path33 from "path";
+import fs41 from "fs";
+import path34 from "path";
 import chalk19 from "chalk";
 import ora6 from "ora";
 
@@ -10968,51 +11139,87 @@ function collectDiff(lastSha) {
   const summary = parts.join(", ") || "no changes";
   return { hasChanges, committedDiff, stagedDiff, unstagedDiff, changedFiles, summary };
 }
+function scopeDiffToDir(diff, dir, allConfigDirs) {
+  if (dir === ".") {
+    const otherDirs = allConfigDirs.filter((d) => d !== ".");
+    if (otherDirs.length === 0) return diff;
+    const changedFiles2 = diff.changedFiles.filter(
+      (f) => !otherDirs.some((d) => f.startsWith(`${d}/`))
+    );
+    const hasChanges2 = changedFiles2.length > 0;
+    return {
+      ...diff,
+      changedFiles: changedFiles2,
+      hasChanges: hasChanges2,
+      summary: hasChanges2 ? `${changedFiles2.length} files changed` : "no changes"
+    };
+  }
+  const prefix = `${dir}/`;
+  const changedFiles = diff.changedFiles.filter((f) => f.startsWith(prefix)).map((f) => f.slice(prefix.length));
+  const hasChanges = changedFiles.length > 0;
+  return {
+    ...diff,
+    changedFiles,
+    hasChanges,
+    summary: hasChanges ? `${changedFiles.length} files changed` : "no changes"
+  };
+}
 
 // src/writers/refresh.ts
 init_pre_commit_block();
 import fs37 from "fs";
 import path30 from "path";
-function writeRefreshDocs(docs) {
+function writeRefreshDocs(docs, dir = ".") {
   const written = [];
+  const p = (relPath) => (dir === "." ? relPath : path30.join(dir, relPath)).replace(/\\/g, "/");
+  const ensureParent = (filePath) => {
+    const parent = path30.dirname(filePath);
+    if (parent !== "." && !fs37.existsSync(parent)) fs37.mkdirSync(parent, { recursive: true });
+  };
   if (docs.agentsMd) {
-    fs37.writeFileSync("AGENTS.md", appendManagedBlocks(docs.agentsMd, "codex"));
-    written.push("AGENTS.md");
+    const filePath = p("AGENTS.md");
+    ensureParent(filePath);
+    fs37.writeFileSync(filePath, appendManagedBlocks(docs.agentsMd, "codex"));
+    written.push(filePath);
   }
   if (docs.claudeMd) {
-    fs37.writeFileSync("CLAUDE.md", appendManagedBlocks(docs.claudeMd));
-    written.push("CLAUDE.md");
+    const filePath = p("CLAUDE.md");
+    ensureParent(filePath);
+    fs37.writeFileSync(filePath, appendManagedBlocks(docs.claudeMd));
+    written.push(filePath);
   }
   if (docs.readmeMd) {
-    fs37.writeFileSync("README.md", docs.readmeMd);
-    written.push("README.md");
+    const filePath = p("README.md");
+    ensureParent(filePath);
+    fs37.writeFileSync(filePath, docs.readmeMd);
+    written.push(filePath);
   }
   if (docs.cursorrules) {
-    fs37.writeFileSync(".cursorrules", docs.cursorrules);
-    written.push(".cursorrules");
+    const filePath = p(".cursorrules");
+    ensureParent(filePath);
+    fs37.writeFileSync(filePath, docs.cursorrules);
+    written.push(filePath);
   }
   if (docs.cursorRules) {
-    const rulesDir = path30.join(".cursor", "rules");
+    const rulesDir = p(path30.join(".cursor", "rules"));
     if (!fs37.existsSync(rulesDir)) fs37.mkdirSync(rulesDir, { recursive: true });
     for (const rule of docs.cursorRules) {
       fs37.writeFileSync(path30.join(rulesDir, rule.filename), rule.content);
-      written.push(`.cursor/rules/${rule.filename}`);
+      written.push(p(path30.join(".cursor", "rules", rule.filename)));
     }
   }
   if (docs.copilotInstructions) {
-    fs37.mkdirSync(".github", { recursive: true });
-    fs37.writeFileSync(
-      path30.join(".github", "copilot-instructions.md"),
-      appendManagedBlocks(docs.copilotInstructions, "copilot")
-    );
-    written.push(".github/copilot-instructions.md");
+    const filePath = p(path30.join(".github", "copilot-instructions.md"));
+    ensureParent(filePath);
+    fs37.writeFileSync(filePath, appendManagedBlocks(docs.copilotInstructions, "copilot"));
+    written.push(filePath);
   }
   if (docs.copilotInstructionFiles) {
-    const instructionsDir = path30.join(".github", "instructions");
-    fs37.mkdirSync(instructionsDir, { recursive: true });
+    const instructionsDir = p(path30.join(".github", "instructions"));
+    if (!fs37.existsSync(instructionsDir)) fs37.mkdirSync(instructionsDir, { recursive: true });
     for (const file of docs.copilotInstructionFiles) {
       fs37.writeFileSync(path30.join(instructionsDir, file.filename), file.content);
-      written.push(`.github/instructions/${file.filename}`);
+      written.push(p(path30.join(".github", "instructions", file.filename)));
     }
   }
   return written;
@@ -11021,8 +11228,15 @@ function writeRefreshDocs(docs) {
 // src/ai/refresh.ts
 init_config();
 init_pre_commit_block();
-async function refreshDocs(diff, existingDocs, projectContext, learnedSection, sources2) {
-  const prompt = buildRefreshPrompt(diff, existingDocs, projectContext, learnedSection, sources2);
+async function refreshDocs(diff, existingDocs, projectContext, learnedSection, sources2, scope) {
+  const prompt = buildRefreshPrompt(
+    diff,
+    existingDocs,
+    projectContext,
+    learnedSection,
+    sources2,
+    scope
+  );
   const fastModel = getFastModel();
   const raw = await llmCall({
     system: REFRESH_SYSTEM_PROMPT,
@@ -11032,8 +11246,14 @@ async function refreshDocs(diff, existingDocs, projectContext, learnedSection, s
   });
   return parseJsonResponse(raw);
 }
-function buildRefreshPrompt(diff, existingDocs, projectContext, learnedSection, sources2) {
+function buildRefreshPrompt(diff, existingDocs, projectContext, learnedSection, sources2, scope) {
   const parts = [];
+  if (scope) {
+    parts.push(`You are updating docs for the \`${scope}\` subdirectory of a monorepo.`);
+    parts.push("Only include changes relevant to files under this directory.");
+    parts.push("The changed files list has been filtered to this directory already.");
+    parts.push("Ignore diff content for files outside this directory.\n");
+  }
   parts.push("Update documentation based on the following code changes.\n");
   if (projectContext.packageName) parts.push(`Project: ${projectContext.packageName}`);
   if (projectContext.languages?.length)
@@ -11315,10 +11535,77 @@ function migrateInlineLearnings() {
 init_config();
 init_resolve_caliber();
 init_builtin_skills();
+
+// src/lib/config-discovery.ts
+import fs39 from "fs";
+import path32 from "path";
+var CONFIG_FILE_MARKERS = [
+  "CLAUDE.md",
+  "AGENTS.md",
+  ".cursorrules",
+  ".github/copilot-instructions.md"
+];
+var CONFIG_DIR_MARKERS = [".cursor/rules", ".github/instructions", ".opencode/skills"];
+var IGNORE_DIRS3 = /* @__PURE__ */ new Set([
+  "node_modules",
+  ".git",
+  ".next",
+  "dist",
+  "build",
+  ".cache",
+  ".turbo",
+  "coverage",
+  ".caliber",
+  "__pycache__",
+  ".venv",
+  "vendor",
+  "target"
+]);
+var MAX_DEPTH = 4;
+function hasConfigFiles(dir) {
+  for (const marker of CONFIG_FILE_MARKERS) {
+    if (fs39.existsSync(path32.join(dir, marker))) return true;
+  }
+  for (const marker of CONFIG_DIR_MARKERS) {
+    const markerPath = path32.join(dir, marker);
+    if (fs39.existsSync(markerPath) && fs39.statSync(markerPath).isDirectory()) return true;
+  }
+  return false;
+}
+function discoverConfigDirs(rootDir) {
+  const dirs = [];
+  if (hasConfigFiles(rootDir)) {
+    dirs.push(".");
+  }
+  walkForConfigs(rootDir, rootDir, 0, dirs);
+  dirs.sort();
+  return dirs;
+}
+function walkForConfigs(baseDir, currentDir, depth, result) {
+  if (depth >= MAX_DEPTH) return;
+  let entries;
+  try {
+    entries = fs39.readdirSync(currentDir, { withFileTypes: true });
+  } catch {
+    return;
+  }
+  for (const entry of entries) {
+    if (!entry.isDirectory()) continue;
+    if (entry.name.startsWith(".") || IGNORE_DIRS3.has(entry.name)) continue;
+    const fullPath = path32.join(currentDir, entry.name);
+    const relPath = path32.relative(baseDir, fullPath).replace(/\\/g, "/");
+    if (hasConfigFiles(fullPath)) {
+      result.push(relPath);
+    }
+    walkForConfigs(baseDir, fullPath, depth + 1, result);
+  }
+}
+
+// src/commands/refresh.ts
 function writeRefreshError(error) {
   try {
-    if (!fs40.existsSync(CALIBER_DIR)) fs40.mkdirSync(CALIBER_DIR, { recursive: true });
-    fs40.writeFileSync(
+    if (!fs41.existsSync(CALIBER_DIR)) fs41.mkdirSync(CALIBER_DIR, { recursive: true });
+    fs41.writeFileSync(
       REFRESH_LAST_ERROR_FILE,
       JSON.stringify(
         {
@@ -11337,15 +11624,15 @@ function writeRefreshError(error) {
 }
 function readRefreshError() {
   try {
-    if (!fs40.existsSync(REFRESH_LAST_ERROR_FILE)) return null;
-    return JSON.parse(fs40.readFileSync(REFRESH_LAST_ERROR_FILE, "utf-8"));
+    if (!fs41.existsSync(REFRESH_LAST_ERROR_FILE)) return null;
+    return JSON.parse(fs41.readFileSync(REFRESH_LAST_ERROR_FILE, "utf-8"));
   } catch {
     return null;
   }
 }
 function clearRefreshError() {
   try {
-    if (fs40.existsSync(REFRESH_LAST_ERROR_FILE)) fs40.unlinkSync(REFRESH_LAST_ERROR_FILE);
+    if (fs41.existsSync(REFRESH_LAST_ERROR_FILE)) fs41.unlinkSync(REFRESH_LAST_ERROR_FILE);
   } catch {
   }
 }
@@ -11354,7 +11641,8 @@ function detectSyncedAgents(writtenFiles) {
   const joined = writtenFiles.join(" ");
   if (joined.includes("CLAUDE.md") || joined.includes(".claude/")) agents.push("Claude Code");
   if (joined.includes(".cursor/") || joined.includes(".cursorrules")) agents.push("Cursor");
-  if (joined.includes("copilot-instructions") || joined.includes(".github/instructions/")) agents.push("Copilot");
+  if (joined.includes("copilot-instructions") || joined.includes(".github/instructions/"))
+    agents.push("Copilot");
   if (joined.includes("AGENTS.md") || joined.includes(".agents/")) agents.push("Codex");
   return agents;
 }
@@ -11364,11 +11652,11 @@ function log2(quiet, ...args) {
 function discoverGitRepos(parentDir) {
   const repos = [];
   try {
-    const entries = fs40.readdirSync(parentDir, { withFileTypes: true });
+    const entries = fs41.readdirSync(parentDir, { withFileTypes: true });
     for (const entry of entries) {
       if (!entry.isDirectory() || entry.name.startsWith(".")) continue;
-      const childPath = path33.join(parentDir, entry.name);
-      if (fs40.existsSync(path33.join(childPath, ".git"))) {
+      const childPath = path34.join(parentDir, entry.name);
+      if (fs41.existsSync(path34.join(childPath, ".git"))) {
         repos.push(childPath);
       }
     }
@@ -11376,51 +11664,33 @@ function discoverGitRepos(parentDir) {
   }
   return repos.sort();
 }
-function collectFilesToWrite(updatedDocs) {
+function collectFilesToWrite(updatedDocs, dir = ".") {
   const files = [];
-  if (updatedDocs.agentsMd) files.push("AGENTS.md");
-  if (updatedDocs.claudeMd) files.push("CLAUDE.md");
-  if (updatedDocs.readmeMd) files.push("README.md");
-  if (updatedDocs.cursorrules) files.push(".cursorrules");
+  const p = (relPath) => (dir === "." ? relPath : path34.join(dir, relPath)).replace(/\\/g, "/");
+  if (updatedDocs.agentsMd) files.push(p("AGENTS.md"));
+  if (updatedDocs.claudeMd) files.push(p("CLAUDE.md"));
+  if (updatedDocs.readmeMd) files.push(p("README.md"));
+  if (updatedDocs.cursorrules) files.push(p(".cursorrules"));
   if (Array.isArray(updatedDocs.cursorRules)) {
     for (const r of updatedDocs.cursorRules)
-      files.push(`.cursor/rules/${r.filename}`);
+      files.push(p(`.cursor/rules/${r.filename}`));
   }
-  if (updatedDocs.copilotInstructions) files.push(".github/copilot-instructions.md");
+  if (updatedDocs.copilotInstructions) files.push(p(".github/copilot-instructions.md"));
   if (Array.isArray(updatedDocs.copilotInstructionFiles)) {
     for (const f of updatedDocs.copilotInstructionFiles)
-      files.push(`.github/instructions/${f.filename}`);
+      files.push(p(`.github/instructions/${f.filename}`));
   }
   return files;
 }
 var REFRESH_COOLDOWN_MS = 3e4;
-async function refreshSingleRepo(repoDir, options) {
+async function refreshDir(repoDir, dir, diff, options) {
   const quiet = !!options.quiet;
   const prefix = options.label ? `${chalk19.bold(options.label)} ` : "";
-  const state = readState();
-  const lastSha = state?.lastRefreshSha ?? null;
-  const currentSha = getCurrentHeadSha();
-  if (state?.lastRefreshTimestamp && lastSha && currentSha === lastSha) {
-    const elapsed = Date.now() - new Date(state.lastRefreshTimestamp).getTime();
-    if (elapsed < REFRESH_COOLDOWN_MS && elapsed > 0) {
-      log2(
-        quiet,
-        chalk19.dim(`${prefix}Skipped \u2014 last refresh was ${Math.round(elapsed / 1e3)}s ago.`)
-      );
-      return;
-    }
-  }
-  const diff = collectDiff(lastSha);
-  if (!diff.hasChanges) {
-    if (currentSha) {
-      writeState({ lastRefreshSha: currentSha, lastRefreshTimestamp: (/* @__PURE__ */ new Date()).toISOString() });
-    }
-    log2(quiet, chalk19.dim(`${prefix}No changes since last refresh.`));
-    return;
-  }
+  const absDir = dir === "." ? repoDir : path34.resolve(repoDir, dir);
+  const scope = dir === "." ? void 0 : dir;
   const spinner = quiet ? null : ora6(`${prefix}Analyzing changes...`).start();
   const learnedSection = readLearnedSection();
-  const fingerprint = await collectFingerprint(repoDir);
+  const fingerprint = await collectFingerprint(absDir);
   const existingDocs = fingerprint.existingConfigs;
   const projectContext = {
     languages: fingerprint.languages,
@@ -11428,8 +11698,8 @@ async function refreshSingleRepo(repoDir, options) {
     packageName: fingerprint.packageName,
     fileTree: fingerprint.fileTree
   };
-  const workspaces = getDetectedWorkspaces(repoDir);
-  const sources2 = resolveAllSources(repoDir, [], workspaces);
+  const workspaces = getDetectedWorkspaces(absDir);
+  const sources2 = resolveAllSources(absDir, [], workspaces);
   const diffPayload = {
     committed: diff.committedDiff,
     staged: diff.stagedDiff,
@@ -11445,7 +11715,8 @@ async function refreshSingleRepo(repoDir, options) {
       existingDocs,
       projectContext,
       learnedSection,
-      sourcesPayload
+      sourcesPayload,
+      scope
     );
   } catch (firstErr) {
     const isTransient = firstErr instanceof Error && TRANSIENT_ERRORS.some((e) => firstErr.message.toLowerCase().includes(e.toLowerCase()));
@@ -11456,7 +11727,8 @@ async function refreshSingleRepo(repoDir, options) {
         existingDocs,
         projectContext,
         learnedSection,
-        sourcesPayload
+        sourcesPayload,
+        scope
       );
     } catch {
       spinner?.fail(`${prefix}Refresh failed after retry`);
@@ -11465,10 +11737,7 @@ async function refreshSingleRepo(repoDir, options) {
   }
   if (!response.docsUpdated || response.docsUpdated.length === 0) {
     spinner?.succeed(`${prefix}No doc updates needed`);
-    if (currentSha) {
-      writeState({ lastRefreshSha: currentSha, lastRefreshTimestamp: (/* @__PURE__ */ new Date()).toISOString() });
-    }
-    return;
+    return { written: [] };
   }
   if (options.dryRun) {
     spinner?.info(`${prefix}Dry run \u2014 would update:`);
@@ -11479,49 +11748,53 @@ async function refreshSingleRepo(repoDir, options) {
       console.log(chalk19.dim(`
   ${response.changesSummary}`));
     }
-    return;
+    return { written: [] };
   }
-  const targetAgent = state?.targetAgent ?? detectTargetAgent(repoDir);
-  const preScore = computeLocalScore(repoDir, targetAgent);
-  const allFilesToWrite = collectFilesToWrite(response.updatedDocs);
+  const allFilesToWrite = collectFilesToWrite(response.updatedDocs, dir);
   const preRefreshContents = /* @__PURE__ */ new Map();
   for (const filePath of allFilesToWrite) {
-    const fullPath = path33.resolve(repoDir, filePath);
+    const fullPath = path34.resolve(repoDir, filePath);
     try {
-      preRefreshContents.set(filePath, fs40.readFileSync(fullPath, "utf-8"));
+      preRefreshContents.set(filePath, fs41.readFileSync(fullPath, "utf-8"));
     } catch {
       preRefreshContents.set(filePath, null);
     }
   }
-  const written = writeRefreshDocs(response.updatedDocs);
+  const state = readState();
+  const targetAgent = state?.targetAgent ?? detectTargetAgent(repoDir);
+  const runQualityGate = dir === ".";
+  const preScore = runQualityGate ? computeLocalScore(absDir, targetAgent) : null;
+  const written = writeRefreshDocs(response.updatedDocs, dir);
   const trigger = quiet ? "hook" : "manual";
   trackRefreshCompleted(written.length, Date.now(), trigger);
-  const postScore = computeLocalScore(repoDir, targetAgent);
-  if (postScore.score < preScore.score) {
-    for (const [filePath, content] of preRefreshContents) {
-      const fullPath = path33.resolve(repoDir, filePath);
-      if (content === null) {
-        try {
-          fs40.unlinkSync(fullPath);
-        } catch {
+  if (runQualityGate && preScore) {
+    const postScore = computeLocalScore(absDir, targetAgent);
+    if (postScore.score < preScore.score) {
+      for (const [filePath, content] of preRefreshContents) {
+        const fullPath = path34.resolve(repoDir, filePath);
+        if (content === null) {
+          try {
+            fs41.unlinkSync(fullPath);
+          } catch {
+          }
+        } else {
+          fs41.writeFileSync(fullPath, content);
         }
-      } else {
-        fs40.writeFileSync(fullPath, content);
       }
+      spinner?.warn(
+        `${prefix}Refresh reverted \u2014 score would drop from ${preScore.score} to ${postScore.score}`
+      );
+      log2(quiet, chalk19.dim(`  Config quality gate prevented a regression. No files were changed.`));
+      return { written: [] };
     }
-    spinner?.warn(
-      `${prefix}Refresh reverted \u2014 score would drop from ${preScore.score} to ${postScore.score}`
-    );
-    log2(quiet, chalk19.dim(`  Config quality gate prevented a regression. No files were changed.`));
-    if (currentSha) {
-      writeState({ lastRefreshSha: currentSha, lastRefreshTimestamp: (/* @__PURE__ */ new Date()).toISOString() });
-    }
-    return;
+    recordScore(postScore, "refresh");
   }
-  recordScore(postScore, "refresh");
   spinner?.succeed(`${prefix}Updated ${written.length} doc${written.length === 1 ? "" : "s"}`);
   const fileChangesMap = new Map(
-    (response.fileChanges || []).map((fc) => [fc.file, fc.description])
+    (response.fileChanges || []).map((fc) => [
+      fc.file,
+      fc.description
+    ])
   );
   for (const file of written) {
     const desc = fileChangesMap.get(file);
@@ -11537,6 +11810,59 @@ async function refreshSingleRepo(repoDir, options) {
     log2(quiet, chalk19.dim(`
   ${response.changesSummary}`));
   }
+  return { written };
+}
+async function refreshSingleRepo(repoDir, options) {
+  const quiet = !!options.quiet;
+  const prefix = options.label ? `${chalk19.bold(options.label)} ` : "";
+  const state = readState();
+  const lastSha = state?.lastRefreshSha ?? null;
+  const currentSha = getCurrentHeadSha();
+  if (state?.lastRefreshTimestamp && lastSha && currentSha === lastSha) {
+    const elapsed = Date.now() - new Date(state.lastRefreshTimestamp).getTime();
+    if (elapsed < REFRESH_COOLDOWN_MS && elapsed > 0) {
+      log2(
+        quiet,
+        chalk19.dim(`${prefix}Skipped \u2014 last refresh was ${Math.round(elapsed / 1e3)}s ago.`)
+      );
+      return;
+    }
+  }
+  const diff = collectDiff(lastSha);
+  if (!diff.hasChanges) {
+    if (currentSha) {
+      writeState({ lastRefreshSha: currentSha, lastRefreshTimestamp: (/* @__PURE__ */ new Date()).toISOString() });
+    }
+    log2(quiet, chalk19.dim(`${prefix}No changes since last refresh.`));
+    return;
+  }
+  const configDirs = discoverConfigDirs(repoDir);
+  if (configDirs.length <= 1) {
+    await refreshDir(repoDir, ".", diff, options);
+  } else {
+    log2(quiet, chalk19.dim(`${prefix}Found configs in ${configDirs.length} directories
+`));
+    let hadFailure = false;
+    for (const dir of configDirs) {
+      const scopedDiff = scopeDiffToDir(diff, dir, configDirs);
+      if (!scopedDiff.hasChanges) continue;
+      const dirLabel = dir === "." ? "root" : dir;
+      try {
+        await refreshDir(repoDir, dir, scopedDiff, { ...options, label: dirLabel });
+      } catch (err) {
+        hadFailure = true;
+        log2(
+          quiet,
+          chalk19.yellow(
+            `  ${dirLabel}: refresh failed \u2014 ${err instanceof Error ? err.message : "unknown error"}`
+          )
+        );
+      }
+    }
+    if (hadFailure) {
+      return;
+    }
+  }
   const builtinWritten = ensureBuiltinSkills();
   for (const file of builtinWritten) {
     log2(quiet, `  ${chalk19.green("\u2713")} ${file} ${chalk19.dim("(built-in)")}`);
@@ -11593,7 +11919,7 @@ async function refreshCommand(options) {
 `));
     const originalDir = process.cwd();
     for (const repo of repos) {
-      const repoName = path33.basename(repo);
+      const repoName = path34.basename(repo);
       try {
         process.chdir(repo);
         await refreshSingleRepo(repo, { ...options, label: repoName });
@@ -11621,7 +11947,7 @@ async function refreshCommand(options) {
 
 // src/commands/hooks.ts
 import chalk20 from "chalk";
-import fs41 from "fs";
+import fs42 from "fs";
 var HOOKS = [
   {
     id: "session-end",
@@ -11665,11 +11991,11 @@ async function hooksCommand(options) {
         console.log(chalk20.green("  \u2713") + ` ${hook.label} enabled`);
       }
     }
-    if (fs41.existsSync(".claude")) {
+    if (fs42.existsSync(".claude")) {
       const r = installLearningHooks();
       if (r.installed) console.log(chalk20.green("  \u2713") + " Claude Code learning hooks enabled");
     }
-    if (fs41.existsSync(".cursor")) {
+    if (fs42.existsSync(".cursor")) {
       const r = installCursorLearningHooks();
       if (r.installed) console.log(chalk20.green("  \u2713") + " Cursor learning hooks enabled");
     }
@@ -11837,8 +12163,8 @@ async function configCommand() {
 }
 
 // src/commands/learn.ts
-import fs45 from "fs";
-import path37 from "path";
+import fs46 from "fs";
+import path38 from "path";
 import chalk23 from "chalk";
 
 // src/learner/stdin.ts
@@ -11869,8 +12195,8 @@ function readStdin() {
 }
 
 // src/learner/storage.ts
-import fs42 from "fs";
-import path34 from "path";
+import fs43 from "fs";
+import path35 from "path";
 var MAX_RESPONSE_LENGTH = 2e3;
 var DEFAULT_STATE = {
   sessionId: null,
@@ -11879,15 +12205,15 @@ var DEFAULT_STATE = {
   lastAnalysisEventCount: 0
 };
 function ensureLearningDir() {
-  if (!fs42.existsSync(getLearningDir())) {
-    fs42.mkdirSync(getLearningDir(), { recursive: true });
+  if (!fs43.existsSync(getLearningDir())) {
+    fs43.mkdirSync(getLearningDir(), { recursive: true });
   }
 }
 function sessionFilePath() {
-  return path34.join(getLearningDir(), LEARNING_SESSION_FILE);
+  return path35.join(getLearningDir(), LEARNING_SESSION_FILE);
 }
 function stateFilePath() {
-  return path34.join(getLearningDir(), LEARNING_STATE_FILE);
+  return path35.join(getLearningDir(), LEARNING_STATE_FILE);
 }
 function truncateResponse(response) {
   const str = JSON.stringify(response);
@@ -11897,10 +12223,10 @@ function truncateResponse(response) {
 function trimSessionFileIfNeeded(filePath) {
   const state = readState2();
   if (state.eventCount + 1 > LEARNING_MAX_EVENTS) {
-    const lines = fs42.readFileSync(filePath, "utf-8").split("\n").filter(Boolean);
+    const lines = fs43.readFileSync(filePath, "utf-8").split("\n").filter(Boolean);
     if (lines.length > LEARNING_MAX_EVENTS) {
       const kept = lines.slice(lines.length - LEARNING_MAX_EVENTS);
-      fs42.writeFileSync(filePath, kept.join("\n") + "\n");
+      fs43.writeFileSync(filePath, kept.join("\n") + "\n");
     }
   }
 }
@@ -11908,19 +12234,19 @@ function appendEvent(event) {
   ensureLearningDir();
   const truncated = { ...event, tool_response: truncateResponse(event.tool_response) };
   const filePath = sessionFilePath();
-  fs42.appendFileSync(filePath, JSON.stringify(truncated) + "\n");
+  fs43.appendFileSync(filePath, JSON.stringify(truncated) + "\n");
   trimSessionFileIfNeeded(filePath);
 }
 function appendPromptEvent(event) {
   ensureLearningDir();
   const filePath = sessionFilePath();
-  fs42.appendFileSync(filePath, JSON.stringify(event) + "\n");
+  fs43.appendFileSync(filePath, JSON.stringify(event) + "\n");
   trimSessionFileIfNeeded(filePath);
 }
 function readAllEvents() {
   const filePath = sessionFilePath();
-  if (!fs42.existsSync(filePath)) return [];
-  const lines = fs42.readFileSync(filePath, "utf-8").split("\n").filter(Boolean);
+  if (!fs43.existsSync(filePath)) return [];
+  const lines = fs43.readFileSync(filePath, "utf-8").split("\n").filter(Boolean);
   const events = [];
   for (const line of lines) {
     try {
@@ -11932,26 +12258,26 @@ function readAllEvents() {
 }
 function getEventCount() {
   const filePath = sessionFilePath();
-  if (!fs42.existsSync(filePath)) return 0;
-  const content = fs42.readFileSync(filePath, "utf-8");
+  if (!fs43.existsSync(filePath)) return 0;
+  const content = fs43.readFileSync(filePath, "utf-8");
   return content.split("\n").filter(Boolean).length;
 }
 function clearSession() {
   const filePath = sessionFilePath();
-  if (fs42.existsSync(filePath)) fs42.unlinkSync(filePath);
+  if (fs43.existsSync(filePath)) fs43.unlinkSync(filePath);
 }
 function readState2() {
   const filePath = stateFilePath();
-  if (!fs42.existsSync(filePath)) return { ...DEFAULT_STATE };
+  if (!fs43.existsSync(filePath)) return { ...DEFAULT_STATE };
   try {
-    return JSON.parse(fs42.readFileSync(filePath, "utf-8"));
+    return JSON.parse(fs43.readFileSync(filePath, "utf-8"));
   } catch {
     return { ...DEFAULT_STATE };
   }
 }
 function writeState2(state) {
   ensureLearningDir();
-  fs42.writeFileSync(stateFilePath(), JSON.stringify(state, null, 2));
+  fs43.writeFileSync(stateFilePath(), JSON.stringify(state, null, 2));
 }
 function resetState() {
   writeState2({ ...DEFAULT_STATE });
@@ -11959,16 +12285,16 @@ function resetState() {
 var LOCK_FILE = "finalize.lock";
 var LOCK_STALE_MS = 5 * 60 * 1e3;
 function lockFilePath() {
-  return path34.join(getLearningDir(), LOCK_FILE);
+  return path35.join(getLearningDir(), LOCK_FILE);
 }
 function acquireFinalizeLock() {
   ensureLearningDir();
   const lockPath = lockFilePath();
-  if (fs42.existsSync(lockPath)) {
+  if (fs43.existsSync(lockPath)) {
     try {
-      const stat = fs42.statSync(lockPath);
+      const stat = fs43.statSync(lockPath);
       if (Date.now() - stat.mtimeMs < LOCK_STALE_MS) {
-        const pid = parseInt(fs42.readFileSync(lockPath, "utf-8").trim(), 10);
+        const pid = parseInt(fs43.readFileSync(lockPath, "utf-8").trim(), 10);
         if (!isNaN(pid) && isProcessAlive(pid)) {
           return false;
         }
@@ -11976,12 +12302,12 @@ function acquireFinalizeLock() {
     } catch {
     }
     try {
-      fs42.unlinkSync(lockPath);
+      fs43.unlinkSync(lockPath);
     } catch {
     }
   }
   try {
-    fs42.writeFileSync(lockPath, String(process.pid), { flag: "wx" });
+    fs43.writeFileSync(lockPath, String(process.pid), { flag: "wx" });
     return true;
   } catch {
     return false;
@@ -11998,30 +12324,30 @@ function isProcessAlive(pid) {
 function releaseFinalizeLock() {
   const lockPath = lockFilePath();
   try {
-    if (fs42.existsSync(lockPath)) fs42.unlinkSync(lockPath);
+    if (fs43.existsSync(lockPath)) fs43.unlinkSync(lockPath);
   } catch {
   }
 }
 
 // src/lib/notifications.ts
-import fs43 from "fs";
-import path35 from "path";
+import fs44 from "fs";
+import path36 from "path";
 import chalk22 from "chalk";
 function notificationFilePath() {
-  return path35.join(getLearningDir(), "last-finalize-summary.json");
+  return path36.join(getLearningDir(), "last-finalize-summary.json");
 }
 function writeFinalizeSummary(summary) {
   try {
     ensureLearningDir();
-    fs43.writeFileSync(notificationFilePath(), JSON.stringify(summary, null, 2));
+    fs44.writeFileSync(notificationFilePath(), JSON.stringify(summary, null, 2));
   } catch {
   }
 }
 function checkPendingNotifications() {
   try {
-    if (!fs43.existsSync(notificationFilePath())) return;
-    const raw = fs43.readFileSync(notificationFilePath(), "utf-8");
-    fs43.unlinkSync(notificationFilePath());
+    if (!fs44.existsSync(notificationFilePath())) return;
+    const raw = fs44.readFileSync(notificationFilePath(), "utf-8");
+    fs44.unlinkSync(notificationFilePath());
     const summary = JSON.parse(raw);
     if (!summary.newItemCount || summary.newItemCount === 0) return;
     const wasteLabel = summary.wasteTokens > 0 ? ` (~${summary.wasteTokens.toLocaleString()} wasted tokens captured)` : "";
@@ -12037,7 +12363,7 @@ function checkPendingNotifications() {
     console.log("");
   } catch {
     try {
-      fs43.unlinkSync(notificationFilePath());
+      fs44.unlinkSync(notificationFilePath());
     } catch {
     }
   }
@@ -12189,8 +12515,8 @@ function calculateSessionWaste(events) {
 init_config();
 
 // src/learner/roi.ts
-import fs44 from "fs";
-import path36 from "path";
+import fs45 from "fs";
+import path37 from "path";
 var DEFAULT_TOTALS = {
   totalWasteTokens: 0,
   totalWasteSeconds: 0,
@@ -12204,19 +12530,19 @@ var DEFAULT_TOTALS = {
   lastSessionTimestamp: ""
 };
 function roiFilePath() {
-  return path36.join(getLearningDir(), LEARNING_ROI_FILE);
+  return path37.join(getLearningDir(), LEARNING_ROI_FILE);
 }
 function readROIStats() {
   const filePath = roiFilePath();
-  if (!fs44.existsSync(filePath)) {
+  if (!fs45.existsSync(filePath)) {
     return { learnings: [], sessions: [], totals: { ...DEFAULT_TOTALS } };
   }
   try {
-    return JSON.parse(fs44.readFileSync(filePath, "utf-8"));
+    return JSON.parse(fs45.readFileSync(filePath, "utf-8"));
   } catch {
     try {
       const corruptPath = filePath + ".corrupt";
-      fs44.renameSync(filePath, corruptPath);
+      fs45.renameSync(filePath, corruptPath);
       console.error(`caliber: roi-stats.json was corrupt \u2014 renamed to ${corruptPath}`);
     } catch {
     }
@@ -12225,7 +12551,7 @@ function readROIStats() {
 }
 function writeROIStats(stats) {
   ensureLearningDir();
-  fs44.writeFileSync(roiFilePath(), JSON.stringify(stats, null, 2));
+  fs45.writeFileSync(roiFilePath(), JSON.stringify(stats, null, 2));
 }
 function recalculateTotals(stats) {
   const totals = stats.totals;
@@ -12434,9 +12760,9 @@ var AUTO_SETTLE_MS = 200;
 var INCREMENTAL_INTERVAL = 50;
 function writeFinalizeError(message) {
   try {
-    const errorPath = path37.join(getLearningDir(), LEARNING_LAST_ERROR_FILE);
-    if (!fs45.existsSync(getLearningDir())) fs45.mkdirSync(getLearningDir(), { recursive: true });
-    fs45.writeFileSync(errorPath, JSON.stringify({
+    const errorPath = path38.join(getLearningDir(), LEARNING_LAST_ERROR_FILE);
+    if (!fs46.existsSync(getLearningDir())) fs46.mkdirSync(getLearningDir(), { recursive: true });
+    fs46.writeFileSync(errorPath, JSON.stringify({
       timestamp: (/* @__PURE__ */ new Date()).toISOString(),
       error: message,
       pid: process.pid
@@ -12446,9 +12772,9 @@ function writeFinalizeError(message) {
 }
 function readFinalizeError() {
   try {
-    const errorPath = path37.join(getLearningDir(), LEARNING_LAST_ERROR_FILE);
-    if (!fs45.existsSync(errorPath)) return null;
-    return JSON.parse(fs45.readFileSync(errorPath, "utf-8"));
+    const errorPath = path38.join(getLearningDir(), LEARNING_LAST_ERROR_FILE);
+    if (!fs46.existsSync(errorPath)) return null;
+    return JSON.parse(fs46.readFileSync(errorPath, "utf-8"));
   } catch {
     return null;
   }
@@ -12495,14 +12821,14 @@ async function learnObserveCommand(options) {
         const { resolveCaliber: resolveCaliber2 } = await Promise.resolve().then(() => (init_resolve_caliber(), resolve_caliber_exports));
         const bin = resolveCaliber2();
         const { spawn: spawn4 } = await import("child_process");
-        const logPath = path37.join(getLearningDir(), LEARNING_FINALIZE_LOG);
-        if (!fs45.existsSync(getLearningDir())) fs45.mkdirSync(getLearningDir(), { recursive: true });
-        const logFd = fs45.openSync(logPath, "a");
+        const logPath = path38.join(getLearningDir(), LEARNING_FINALIZE_LOG);
+        if (!fs46.existsSync(getLearningDir())) fs46.mkdirSync(getLearningDir(), { recursive: true });
+        const logFd = fs46.openSync(logPath, "a");
         spawn4(bin, ["learn", "finalize", "--auto", "--incremental"], {
           detached: true,
           stdio: ["ignore", logFd, logFd]
         }).unref();
-        fs45.closeSync(logFd);
+        fs46.closeSync(logFd);
       } catch {
       }
     }
@@ -12709,7 +13035,7 @@ async function learnFinalizeCommand(options) {
 }
 async function learnInstallCommand() {
   let anyInstalled = false;
-  if (fs45.existsSync(".claude")) {
+  if (fs46.existsSync(".claude")) {
     const r = installLearningHooks();
     if (r.installed) {
       console.log(chalk23.green("\u2713") + " Claude Code learning hooks installed");
@@ -12718,7 +13044,7 @@ async function learnInstallCommand() {
       console.log(chalk23.dim("  Claude Code hooks already installed"));
     }
   }
-  if (fs45.existsSync(".cursor")) {
+  if (fs46.existsSync(".cursor")) {
     const r = installCursorLearningHooks();
     if (r.installed) {
       console.log(chalk23.green("\u2713") + " Cursor learning hooks installed");
@@ -12727,7 +13053,7 @@ async function learnInstallCommand() {
       console.log(chalk23.dim("  Cursor hooks already installed"));
     }
   }
-  if (!fs45.existsSync(".claude") && !fs45.existsSync(".cursor")) {
+  if (!fs46.existsSync(".claude") && !fs46.existsSync(".cursor")) {
     console.log(chalk23.yellow("No .claude/ or .cursor/ directory found."));
     console.log(chalk23.dim(`  Run \`${resolveCaliber()} init\` first, or create the directory manually.`));
     return;
@@ -12785,8 +13111,8 @@ async function learnStatusCommand() {
   if (lastError) {
     console.log(`Last error: ${chalk23.red(lastError.error)}`);
     console.log(chalk23.dim(`  at ${lastError.timestamp}`));
-    const logPath = path37.join(getLearningDir(), LEARNING_FINALIZE_LOG);
-    if (fs45.existsSync(logPath)) {
+    const logPath = path38.join(getLearningDir(), LEARNING_FINALIZE_LOG);
+    if (fs46.existsSync(logPath)) {
       console.log(chalk23.dim(`  Full log: ${logPath}`));
     }
   }
@@ -12866,11 +13192,11 @@ async function learnDeleteCommand(indexStr) {
   }
   const item = items[targetIdx];
   const filePath = item.source === "personal" ? PERSONAL_LEARNINGS_FILE : "CALIBER_LEARNINGS.md";
-  if (!fs45.existsSync(filePath)) {
+  if (!fs46.existsSync(filePath)) {
     console.log(chalk23.red("Learnings file not found."));
     return;
   }
-  const content = fs45.readFileSync(filePath, "utf-8");
+  const content = fs46.readFileSync(filePath, "utf-8");
   const lines = content.split("\n");
   const bulletsOfSource = items.filter((i) => i.source === item.source);
   const posInFile = bulletsOfSource.indexOf(item);
@@ -12891,9 +13217,9 @@ async function learnDeleteCommand(indexStr) {
   }
   const bulletToRemove = lines[lineToRemove];
   const newLines = lines.filter((_, i) => i !== lineToRemove);
-  fs45.writeFileSync(filePath, newLines.join("\n"));
+  fs46.writeFileSync(filePath, newLines.join("\n"));
   if (item.source === "personal") {
-    fs45.chmodSync(filePath, 384);
+    fs46.chmodSync(filePath, 384);
   }
   const roiStats = readROIStats();
   const cleanText = bulletToRemove.replace(/^- /, "").replace(/^\*\*\[[^\]]+\]\*\*\s*/, "").trim();
@@ -13066,8 +13392,8 @@ async function insightsCommand(options) {
 }
 
 // src/commands/sources.ts
-import fs46 from "fs";
-import path38 from "path";
+import fs47 from "fs";
+import path39 from "path";
 import chalk25 from "chalk";
 init_resolve_caliber();
 async function sourcesListCommand() {
@@ -13084,9 +13410,9 @@ async function sourcesListCommand() {
   if (configSources.length > 0) {
     for (const source of configSources) {
       const sourcePath = source.path || source.url || "";
-      const exists = source.path ? fs46.existsSync(path38.resolve(dir, source.path)) : false;
+      const exists = source.path ? fs47.existsSync(path39.resolve(dir, source.path)) : false;
       const status = exists ? chalk25.green("reachable") : chalk25.red("not found");
-      const hasSummary = source.path && fs46.existsSync(path38.join(path38.resolve(dir, source.path), ".caliber", "summary.json"));
+      const hasSummary = source.path && fs47.existsSync(path39.join(path39.resolve(dir, source.path), ".caliber", "summary.json"));
       console.log(`  ${chalk25.bold(source.role || source.type)}  ${chalk25.dim(sourcePath)}`);
       console.log(`    Type: ${source.type}  Status: ${status}${hasSummary ? "  " + chalk25.cyan("has summary.json") : ""}`);
       if (source.description) console.log(`    ${chalk25.dim(source.description)}`);
@@ -13096,7 +13422,7 @@ async function sourcesListCommand() {
   if (workspaces.length > 0) {
     console.log(chalk25.dim("  Auto-detected workspaces:"));
     for (const ws of workspaces) {
-      const exists = fs46.existsSync(path38.resolve(dir, ws));
+      const exists = fs47.existsSync(path39.resolve(dir, ws));
       console.log(`    ${exists ? chalk25.green("\u25CF") : chalk25.red("\u25CF")} ${ws}`);
     }
     console.log("");
@@ -13104,8 +13430,8 @@ async function sourcesListCommand() {
 }
 async function sourcesAddCommand(sourcePath) {
   const dir = process.cwd();
-  const absPath = path38.resolve(dir, sourcePath);
-  if (!fs46.existsSync(absPath)) {
+  const absPath = path39.resolve(dir, sourcePath);
+  if (!fs47.existsSync(absPath)) {
     console.log(chalk25.red(`
   Path not found: ${sourcePath}
 `));
@@ -13120,7 +13446,7 @@ async function sourcesAddCommand(sourcePath) {
   }
   const existing = loadSourcesConfig(dir);
   const alreadyConfigured = existing.some(
-    (s) => s.path && path38.resolve(dir, s.path) === absPath
+    (s) => s.path && path39.resolve(dir, s.path) === absPath
   );
   if (alreadyConfigured) {
     console.log(chalk25.yellow(`
@@ -13168,8 +13494,8 @@ async function sourcesRemoveCommand(name) {
 }
 
 // src/commands/publish.ts
-import fs47 from "fs";
-import path39 from "path";
+import fs48 from "fs";
+import path40 from "path";
 import chalk26 from "chalk";
 import ora7 from "ora";
 init_config();
@@ -13184,10 +13510,10 @@ async function publishCommand() {
   const spinner = ora7("Generating project summary...").start();
   try {
     const fingerprint = await collectFingerprint(dir);
-    const claudeMd = readFileOrNull(path39.join(dir, "CLAUDE.md"));
+    const claudeMd = readFileOrNull(path40.join(dir, "CLAUDE.md"));
     const topLevelDirs = fingerprint.fileTree.filter((f) => f.endsWith("/") && !f.includes("/")).map((f) => f.replace(/\/$/, ""));
     const summary = {
-      name: fingerprint.packageName || path39.basename(dir),
+      name: fingerprint.packageName || path40.basename(dir),
       version: "1.0.0",
       description: fingerprint.description || "",
       languages: fingerprint.languages,
@@ -13199,7 +13525,7 @@ async function publishCommand() {
       summary.conventions = claudeMd.slice(0, 2e3);
     }
     try {
-      const pkgContent = readFileOrNull(path39.join(dir, "package.json"));
+      const pkgContent = readFileOrNull(path40.join(dir, "package.json"));
       if (pkgContent) {
         const pkg3 = JSON.parse(pkgContent);
         if (pkg3.scripts) {
@@ -13212,14 +13538,14 @@ async function publishCommand() {
       }
     } catch {
     }
-    const outputDir = path39.join(dir, ".caliber");
-    if (!fs47.existsSync(outputDir)) {
-      fs47.mkdirSync(outputDir, { recursive: true });
+    const outputDir = path40.join(dir, ".caliber");
+    if (!fs48.existsSync(outputDir)) {
+      fs48.mkdirSync(outputDir, { recursive: true });
     }
-    const outputPath = path39.join(outputDir, "summary.json");
-    fs47.writeFileSync(outputPath, JSON.stringify(summary, null, 2) + "\n", "utf-8");
+    const outputPath = path40.join(outputDir, "summary.json");
+    fs48.writeFileSync(outputPath, JSON.stringify(summary, null, 2) + "\n", "utf-8");
     spinner.succeed("Project summary published");
-    console.log(`  ${chalk26.green("\u2713")} ${path39.relative(dir, outputPath)}`);
+    console.log(`  ${chalk26.green("\u2713")} ${path40.relative(dir, outputPath)}`);
     console.log(chalk26.dim("\n  Other projects can now reference this repo as a source."));
     console.log(chalk26.dim("  When they run `caliber init`, they'll read this summary automatically.\n"));
   } catch (err) {
@@ -13232,7 +13558,7 @@ async function publishCommand() {
 
 // src/commands/bootstrap.ts
 init_builtin_skills();
-import fs48 from "fs";
+import fs49 from "fs";
 import chalk27 from "chalk";
 var PLATFORM_SKILL_DIRS = {
   claude: ".claude/skills",
@@ -13253,8 +13579,8 @@ async function bootstrapCommand() {
     for (const skill of BUILTIN_SKILLS) {
       const skillDir = `${skillsDir}/${skill.name}`;
       const skillPath = `${skillDir}/SKILL.md`;
-      fs48.mkdirSync(skillDir, { recursive: true });
-      fs48.writeFileSync(skillPath, buildSkillContent(skill));
+      fs49.mkdirSync(skillDir, { recursive: true });
+      fs49.writeFileSync(skillPath, buildSkillContent(skill));
       written.push(skillPath);
     }
   }
@@ -13271,8 +13597,8 @@ async function bootstrapCommand() {
 }
 
 // src/commands/uninstall.ts
-import fs49 from "fs";
-import path40 from "path";
+import fs50 from "fs";
+import path41 from "path";
 import chalk28 from "chalk";
 import confirm3 from "@inquirer/confirm";
 init_pre_commit_block();
@@ -13280,18 +13606,18 @@ init_builtin_skills();
 init_config();
 var MANAGED_DOC_FILES = [
   "CLAUDE.md",
-  path40.join(".github", "copilot-instructions.md"),
+  path41.join(".github", "copilot-instructions.md"),
   "AGENTS.md"
 ];
 var SKILL_DIRS = PLATFORM_CONFIGS.map((c) => c.skillsDir);
-var CURSOR_RULES_DIR = path40.join(".cursor", "rules");
+var CURSOR_RULES_DIR = path41.join(".cursor", "rules");
 function removeCaliberCursorRules() {
   const removed = [];
-  if (!fs49.existsSync(CURSOR_RULES_DIR)) return removed;
-  for (const file of fs49.readdirSync(CURSOR_RULES_DIR)) {
+  if (!fs50.existsSync(CURSOR_RULES_DIR)) return removed;
+  for (const file of fs50.readdirSync(CURSOR_RULES_DIR)) {
     if (file.startsWith("caliber-") && file.endsWith(".mdc")) {
-      const fullPath = path40.join(CURSOR_RULES_DIR, file);
-      fs49.unlinkSync(fullPath);
+      const fullPath = path41.join(CURSOR_RULES_DIR, file);
+      fs50.unlinkSync(fullPath);
       removed.push(fullPath);
     }
   }
@@ -13300,11 +13626,11 @@ function removeCaliberCursorRules() {
 function removeBuiltinSkills() {
   const removed = [];
   for (const skillsDir of SKILL_DIRS) {
-    if (!fs49.existsSync(skillsDir)) continue;
+    if (!fs50.existsSync(skillsDir)) continue;
     for (const name of BUILTIN_SKILL_NAMES) {
-      const skillDir = path40.join(skillsDir, name);
-      if (fs49.existsSync(skillDir)) {
-        fs49.rmSync(skillDir, { recursive: true });
+      const skillDir = path41.join(skillsDir, name);
+      if (fs50.existsSync(skillDir)) {
+        fs50.rmSync(skillDir, { recursive: true });
         removed.push(skillDir);
       }
     }
@@ -13314,15 +13640,15 @@ function removeBuiltinSkills() {
 function stripManagedBlocksFromFiles() {
   const modified = [];
   for (const filePath of MANAGED_DOC_FILES) {
-    if (!fs49.existsSync(filePath)) continue;
-    const original = fs49.readFileSync(filePath, "utf-8");
+    if (!fs50.existsSync(filePath)) continue;
+    const original = fs50.readFileSync(filePath, "utf-8");
     const stripped = stripManagedBlocks(original);
     if (stripped !== original) {
       const trimmed = stripped.trim();
       if (!trimmed || /^#\s*\S*$/.test(trimmed)) {
-        fs49.unlinkSync(filePath);
+        fs50.unlinkSync(filePath);
       } else {
-        fs49.writeFileSync(filePath, stripped);
+        fs50.writeFileSync(filePath, stripped);
       }
       modified.push(filePath);
     }
@@ -13330,8 +13656,8 @@ function stripManagedBlocksFromFiles() {
   return modified;
 }
 function removeDirectory(dir) {
-  if (!fs49.existsSync(dir)) return false;
-  fs49.rmSync(dir, { recursive: true });
+  if (!fs50.existsSync(dir)) return false;
+  fs50.rmSync(dir, { recursive: true });
   return true;
 }
 async function uninstallCommand(options) {
@@ -13388,8 +13714,8 @@ async function uninstallCommand(options) {
     console.log(`  ${chalk28.red("\u2717")} ${skill}/`);
   }
   if (removedSkills.length > 0) actions.push("builtin skills");
-  if (fs49.existsSync("CALIBER_LEARNINGS.md")) {
-    fs49.unlinkSync("CALIBER_LEARNINGS.md");
+  if (fs50.existsSync("CALIBER_LEARNINGS.md")) {
+    fs50.unlinkSync("CALIBER_LEARNINGS.md");
     console.log(`  ${chalk28.red("\u2717")} CALIBER_LEARNINGS.md`);
     actions.push("learnings file");
   }
@@ -13403,18 +13729,18 @@ async function uninstallCommand(options) {
   }
   trackUninstallExecuted();
   const configPath = getConfigFilePath();
-  if (fs49.existsSync(configPath)) {
+  if (fs50.existsSync(configPath)) {
     console.log("");
     const removeConfig = options.force || await confirm3({
       message: `Remove global config (~/.caliber/config.json)? This affects all projects.`
     });
     if (removeConfig) {
-      fs49.unlinkSync(configPath);
+      fs50.unlinkSync(configPath);
       console.log(`  ${chalk28.red("\u2717")} ${configPath}`);
-      const configDir = path40.dirname(configPath);
+      const configDir = path41.dirname(configPath);
       try {
-        const remaining = fs49.readdirSync(configDir);
-        if (remaining.length === 0) fs49.rmdirSync(configDir);
+        const remaining = fs50.readdirSync(configDir);
+        if (remaining.length === 0) fs50.rmdirSync(configDir);
       } catch {
       }
     }
@@ -13425,10 +13751,8 @@ async function uninstallCommand(options) {
 }
 
 // src/cli.ts
-var __dirname = path41.dirname(fileURLToPath(import.meta.url));
-var pkg = JSON.parse(
-  fs50.readFileSync(path41.resolve(__dirname, "..", "package.json"), "utf-8")
-);
+var __dirname = path42.dirname(fileURLToPath(import.meta.url));
+var pkg = JSON.parse(fs51.readFileSync(path42.resolve(__dirname, "..", "package.json"), "utf-8"));
 var program = new Command();
 var displayVersion = process.env.CALIBER_LOCAL ? `${pkg.version}-local` : pkg.version;
 program.name(process.env.CALIBER_LOCAL ? "caloc" : "caliber").description("AI context infrastructure for coding agents").version(displayVersion).option("--no-traces", "Disable anonymous telemetry for this run");
@@ -13483,22 +13807,38 @@ function parseAgentOption(value) {
   if (value === "both") return ["claude", "cursor"];
   if (value === "all") return ["claude", "cursor", "codex", "opencode", "github-copilot"];
   const valid = ["claude", "cursor", "codex", "opencode", "github-copilot"];
-  const agents = [...new Set(value.split(",").map((s) => s.trim().toLowerCase()).filter((a) => valid.includes(a)))];
+  const agents = [
+    ...new Set(
+      value.split(",").map((s) => s.trim().toLowerCase()).filter((a) => valid.includes(a))
+    )
+  ];
   if (agents.length === 0) {
-    console.error(`Invalid agent "${value}". Choose from: claude, cursor, codex, opencode, github-copilot (comma-separated for multiple)`);
+    console.error(
+      `Invalid agent "${value}". Choose from: claude, cursor, codex, opencode, github-copilot (comma-separated for multiple)`
+    );
     process.exit(1);
   }
   return agents;
 }
-program.command("init").description("Initialize your project for AI-assisted development").option("--agent <type>", "Target agents (comma-separated): claude, cursor, codex, opencode, github-copilot", parseAgentOption).option("--source <paths...>", "Related source paths to include as context").option("--dry-run", "Preview changes without writing files").option("--force", "Overwrite existing config without prompting").option("--debug-report", void 0, false).option("--show-tokens", "Show token usage summary at the end").option("--auto-approve", "Run without interactive prompts (auto-accept all)").option("--verbose", "Show detailed logs of each step").action(tracked("init", initCommand));
-program.command("bootstrap").description("Install agent skills (/setup-caliber, /find-skills, /save-learning) without running init").action(tracked("bootstrap", bootstrapCommand));
+program.command("init").description("Initialize your project for AI-assisted development").option(
+  "--agent <type>",
+  "Target agents (comma-separated): claude, cursor, codex, opencode, github-copilot",
+  parseAgentOption
+).option("--source <paths...>", "Related source paths to include as context").option("--dry-run", "Preview changes without writing files").option("--force", "Overwrite existing config without prompting").option("--debug-report", void 0, false).option("--show-tokens", "Show token usage summary at the end").option("--auto-approve", "Run without interactive prompts (auto-accept all)").option("--verbose", "Show detailed logs of each step").option("--thorough", "Deep analysis \u2014 more refinement passes for maximum quality").action(tracked("init", initCommand));
+program.command("bootstrap").description(
+  "Install agent skills (/setup-caliber, /find-skills, /save-learning) without running init"
+).action(tracked("bootstrap", bootstrapCommand));
 program.command("undo").description("Revert all config changes made by Caliber").action(tracked("undo", undoCommand));
 program.command("uninstall").description("Remove all Caliber resources from this project").option("--force", "Skip confirmation prompt").action(tracked("uninstall", (options) => uninstallCommand(options)));
 program.command("status").description("Show current Caliber config status").option("--json", "Output as JSON").action(tracked("status", statusCommand));
 program.command("regenerate").alias("regen").alias("re").description("Re-analyze project and regenerate config").option("--dry-run", "Preview changes without writing files").action(tracked("regenerate", regenerateCommand));
 program.command("config").description("Configure LLM provider, API key, and model").action(tracked("config", configCommand));
 program.command("skills").description("Discover and install community skills for your project").option("--query <terms>", 'Search for skills by topic (e.g. "react frontend")').option("--install <slugs>", "Install specific skills by slug (comma-separated)").action(tracked("skills", recommendCommand));
-program.command("score").description("Score your AI context configuration (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, opencode, github-copilot", parseAgentOption).option("--compare <ref>", "Compare score against a git ref (branch, tag, or SHA)").action(tracked("score", scoreCommand));
+program.command("score").description("Score your AI context configuration (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, opencode, github-copilot",
+  parseAgentOption
+).option("--compare <ref>", "Compare score against a git ref (branch, tag, or SHA)").action(tracked("score", scoreCommand));
 program.command("refresh").description("Update docs based on recent code changes").option("--quiet", "Suppress output (for use in hooks)").option("--dry-run", "Preview changes without writing files").action(tracked("refresh", refreshCommand));
 program.command("hooks").description("Manage auto-refresh hooks (toggle interactively)").option("--install", "Enable all hooks non-interactively").option("--remove", "Disable all hooks non-interactively").action(tracked("hooks", hooksCommand));
 program.command("insights").description("Show agent performance insights and learning impact").option("--json", "Output as JSON").action(tracked("insights", insightsCommand));
@@ -13509,7 +13849,12 @@ sources.command("remove").description("Remove a configured source").argument("<n
 program.command("publish").description("Generate a machine-readable summary for other repos to consume").action(tracked("publish", publishCommand));
 var learn = program.command("learn").description("Manage session learning \u2014 extract patterns from your AI coding sessions");
 learn.command("observe").description("Record a tool event from stdin (called by hooks)").option("--failure", "Mark event as a tool failure").option("--prompt", "Record a user prompt event").action(tracked("learn:observe", learnObserveCommand));
-learn.command("finalize").description("Analyze session events and update CALIBER_LEARNINGS.md (called on SessionEnd)").option("--force", "Skip the running-process check (for manual invocation)").option("--auto", "Silent mode for hooks (lower threshold, no interactive output)").option("--incremental", "Extract learnings mid-session without clearing events").action(tracked("learn:finalize", (opts) => learnFinalizeCommand(opts)));
+learn.command("finalize").description("Analyze session events and update CALIBER_LEARNINGS.md (called on SessionEnd)").option("--force", "Skip the running-process check (for manual invocation)").option("--auto", "Silent mode for hooks (lower threshold, no interactive output)").option("--incremental", "Extract learnings mid-session without clearing events").action(
+  tracked(
+    "learn:finalize",
+    (opts) => learnFinalizeCommand(opts)
+  )
+);
 learn.command("install").description("Install learning hooks into .claude/settings.json").action(tracked("learn:install", learnInstallCommand));
 learn.command("remove").description("Remove learning hooks from .claude/settings.json").action(tracked("learn:remove", learnRemoveCommand));
 learn.command("status").description("Show learning system status").action(tracked("learn:status", learnStatusCommand));
@@ -13518,15 +13863,15 @@ learn.command("delete <index>").description("Delete a learning by its index numb
 learn.command("add <content>").description("Add a learning directly (used by agent skills)").option("--personal", "Save as a personal learning instead of project-level").action(tracked("learn:add", learnAddCommand));
 
 // src/utils/version-check.ts
-import fs51 from "fs";
-import path42 from "path";
+import fs52 from "fs";
+import path43 from "path";
 import { fileURLToPath as fileURLToPath2 } from "url";
 import { execSync as execSync16, execFileSync as execFileSync3 } from "child_process";
 import chalk29 from "chalk";
 import ora8 from "ora";
 import confirm4 from "@inquirer/confirm";
-var __dirname_vc = path42.dirname(fileURLToPath2(import.meta.url));
-var pkg2 = JSON.parse(fs51.readFileSync(path42.resolve(__dirname_vc, "..", "package.json"), "utf-8"));
+var __dirname_vc = path43.dirname(fileURLToPath2(import.meta.url));
+var pkg2 = JSON.parse(fs52.readFileSync(path43.resolve(__dirname_vc, "..", "package.json"), "utf-8"));
 function getChannel(version) {
   const match = version.match(/-(dev|next)\./);
   return match ? match[1] : "latest";
@@ -13553,8 +13898,8 @@ function getInstalledVersion() {
       encoding: "utf-8",
       stdio: ["pipe", "pipe", "pipe"]
     }).trim();
-    const pkgPath = path42.join(globalRoot, "@rely-ai", "caliber", "package.json");
-    return JSON.parse(fs51.readFileSync(pkgPath, "utf-8")).version;
+    const pkgPath = path43.join(globalRoot, "@rely-ai", "caliber", "package.json");
+    return JSON.parse(fs52.readFileSync(pkgPath, "utf-8")).version;
   } catch {
     return null;
   }