fix: improve error handling, fix bugs, and optimize core libraries

utils.js:
- Fix countInFile: enforce global flag on regex to prevent silent
  under-counting (match() without /g returns only first match)
- Add 5s timeout to readStdinJson to prevent hooks hanging forever
- Handle EEXIST race condition in ensureDir
- Pre-compile regex patterns in getGitModifiedFiles to avoid N*M
  compilations and catch invalid patterns before filtering
- Add JSDoc documentation to all improved functions

session-manager.js:
- Fix getSessionById triple file read: pass pre-read content to
  getSessionStats instead of re-reading from disk
- Allow getSessionStats to accept content string directly

session-aliases.js:
- Wrap temp file cleanup in try/catch to prevent cascading errors

check-console-log.js:
- Refactor to use shared utils (isGitRepo, getGitModifiedFiles, log)
  instead of raw execSync calls
- Add exclusion patterns for test files, config files, and scripts/
  where console.log is intentional

session-end.js:
- Log count of skipped unparseable transcript lines for diagnostics

suggest-compact.js:
- Guard against NaN from corrupted counter files

package-manager.js:
- Remove dead fallbackOrder parameter (unused after #162 fix)

scripts/hooks/check-console-log.js

@@ -2,57 +2,61 @@
 
 /**
  * Stop Hook: Check for console.log statements in modified files
- * 
- * This hook runs after each response and checks if any modified
- * JavaScript/TypeScript files contain console.log statements.
- * It provides warnings to help developers remember to remove
- * debug statements before committing.
+ *
+ * Cross-platform (Windows, macOS, Linux)
+ *
+ * Runs after each response and checks if any modified JavaScript/TypeScript
+ * files contain console.log statements. Provides warnings to help developers
+ * remember to remove debug statements before committing.
+ *
+ * Exclusions: test files, config files, and scripts/ directory (where
+ * console.log is often intentional).
  */
 
-const { execSync } = require('child_process');
 const fs = require('fs');
+const { isGitRepo, getGitModifiedFiles, log } = require('../lib/utils');
+
+// Files where console.log is expected and should not trigger warnings
+const EXCLUDED_PATTERNS = [
+  /\.test\.[jt]sx?$/,
+  /\.spec\.[jt]sx?$/,
+  /\.config\.[jt]s$/,
+  /scripts\//,
+  /__tests__\//,
+  /__mocks__\//,
+];
 
 let data = '';
 
-// Read stdin
 process.stdin.on('data', chunk => {
   data += chunk;
 });
 
 process.stdin.on('end', () => {
   try {
-    // Check if we're in a git repository
-    try {
-      execSync('git rev-parse --git-dir', { stdio: 'pipe' });
-    } catch {
-      // Not in a git repo, just pass through the data
+    if (!isGitRepo()) {
       console.log(data);
       process.exit(0);
     }
 
-    // Get list of modified files
-    const files = execSync('git diff --name-only HEAD', {
-      encoding: 'utf8',
-      stdio: ['pipe', 'pipe', 'pipe']
-    })
-      .split('\n')
-      .filter(f => /\.(ts|tsx|js|jsx)$/.test(f) && fs.existsSync(f));
+    const files = getGitModifiedFiles(['\\.tsx?$', '\\.jsx?$'])
+      .filter(f => fs.existsSync(f))
+      .filter(f => !EXCLUDED_PATTERNS.some(pattern => pattern.test(f)));
 
     let hasConsole = false;
 
-    // Check each file for console.log
     for (const file of files) {
       const content = fs.readFileSync(file, 'utf8');
       if (content.includes('console.log')) {
-        console.error(`[Hook] WARNING: console.log found in ${file}`);
+        log(`[Hook] WARNING: console.log found in ${file}`);
         hasConsole = true;
       }
     }
 
     if (hasConsole) {
-      console.error('[Hook] Remove console.log statements before committing');
+      log('[Hook] Remove console.log statements before committing');
     }
-  } catch (_error) {
+  } catch {
     // Silently ignore errors (git might not be available, etc.)
   }
 

scripts/hooks/session-end.js

@@ -38,6 +38,7 @@ function extractSessionSummary(transcriptPath) {
   const userMessages = [];
   const toolsUsed = new Set();
   const filesModified = new Set();
+  let parseErrors = 0;
 
   for (const line of lines) {
     try {
@@ -66,10 +67,14 @@ function extractSessionSummary(transcriptPath) {
         }
       }
     } catch {
-      // Skip unparseable lines
+      parseErrors++;
     }
   }
 
+  if (parseErrors > 0) {
+    log(`[SessionEnd] Skipped ${parseErrors}/${lines.length} unparseable transcript lines`);
+  }
+
   if (userMessages.length === 0) return null;
 
   return {

scripts/hooks/suggest-compact.js

@@ -23,9 +23,9 @@ const {
 
 async function main() {
   // Track tool call count (increment in a temp file)
-  // Use a session-specific counter file based on PID from parent process
-  // or session ID from environment
-  const sessionId = process.env.CLAUDE_SESSION_ID || process.ppid || 'default';
+  // Use a session-specific counter file based on session ID from environment
+  // or parent PID as fallback
+  const sessionId = process.env.CLAUDE_SESSION_ID || String(process.ppid) || 'default';
   const counterFile = path.join(getTempDir(), `claude-tool-count-${sessionId}`);
   const threshold = parseInt(process.env.COMPACT_THRESHOLD || '50', 10);
 
@@ -34,7 +34,9 @@ async function main() {
   // Read existing count or start at 1
   const existing = readFile(counterFile);
   if (existing) {
-    count = parseInt(existing.trim(), 10) + 1;
+    const parsed = parseInt(existing.trim(), 10);
+    // Guard against NaN from corrupted counter file
+    count = Number.isFinite(parsed) ? parsed + 1 : 1;
   }
 
   // Save updated count

scripts/lib/package-manager.js

@@ -156,11 +156,12 @@ function getAvailablePackageManagers() {
  * 5. Global user preference (in ~/.claude/package-manager.json)
  * 6. Default to npm (no child processes spawned)
  *
- * @param {object} options - { projectDir, fallbackOrder }
+ * @param {object} options - Options
+ * @param {string} options.projectDir - Project directory to detect from (default: cwd)
  * @returns {object} - { name, config, source }
  */
 function getPackageManager(options = {}) {
-  const { projectDir = process.cwd(), fallbackOrder = DETECTION_PRIORITY } = options;
+  const { projectDir = process.cwd() } = options;
 
   // 1. Check environment variable
   const envPm = process.env.CLAUDE_PACKAGE_MANAGER;

scripts/lib/session-aliases.js

@@ -135,9 +135,13 @@ function saveAliases(aliases) {
       }
     }
 
-    // Clean up temp file
-    if (fs.existsSync(tempPath)) {
-      fs.unlinkSync(tempPath);
+    // Clean up temp file (best-effort)
+    try {
+      if (fs.existsSync(tempPath)) {
+        fs.unlinkSync(tempPath);
+      }
+    } catch {
+      // Non-critical: temp file will be overwritten on next save
     }
 
     return false;

scripts/lib/session-manager.js

@@ -143,11 +143,21 @@ function parseSessionMetadata(content) {
 
 /**
  * Calculate statistics for a session
- * @param {string} sessionPath - Full path to session file
+ * @param {string} sessionPathOrContent - Full path to session file, OR
+ *   the pre-read content string (to avoid redundant disk reads when
+ *   the caller already has the content loaded).
  * @returns {object} Statistics object
  */
-function getSessionStats(sessionPath) {
-  const content = getSessionContent(sessionPath);
+function getSessionStats(sessionPathOrContent) {
+  // Accept pre-read content string to avoid redundant file reads.
+  // If the argument looks like a file path (no newlines, ends with .tmp),
+  // read from disk. Otherwise treat it as content.
+  const content = (typeof sessionPathOrContent === 'string' &&
+    !sessionPathOrContent.includes('\n') &&
+    sessionPathOrContent.endsWith('.tmp'))
+    ? getSessionContent(sessionPathOrContent)
+    : sessionPathOrContent;
+
   const metadata = parseSessionMetadata(content);
 
   return {
@@ -281,7 +291,8 @@ function getSessionById(sessionId, includeContent = false) {
     if (includeContent) {
       session.content = getSessionContent(sessionPath);
       session.metadata = parseSessionMetadata(session.content);
-      session.stats = getSessionStats(sessionPath);
+      // Pass pre-read content to avoid a redundant disk read
+      session.stats = getSessionStats(session.content || '');
     }
 
     return session;

scripts/lib/utils.js

@@ -57,10 +57,20 @@ function getTempDir() {
 
 /**
  * Ensure a directory exists (create if not)
+ * @param {string} dirPath - Directory path to create
+ * @returns {string} The directory path
+ * @throws {Error} If directory cannot be created (e.g., permission denied)
  */
 function ensureDir(dirPath) {
-  if (!fs.existsSync(dirPath)) {
-    fs.mkdirSync(dirPath, { recursive: true });
+  try {
+    if (!fs.existsSync(dirPath)) {
+      fs.mkdirSync(dirPath, { recursive: true });
+    }
+  } catch (err) {
+    // EEXIST is fine (race condition with another process creating it)
+    if (err.code !== 'EEXIST') {
+      throw err;
+    }
   }
   return dirPath;
 }
@@ -187,10 +197,29 @@ function findFiles(dir, pattern, options = {}) {
 
 /**
  * Read JSON from stdin (for hook input)
+ * @param {object} options - Options
+ * @param {number} options.timeoutMs - Timeout in milliseconds (default: 5000).
+ *   Prevents hooks from hanging indefinitely if stdin never closes.
+ * @returns {Promise<object>} Parsed JSON object, or empty object if stdin is empty
  */
-async function readStdinJson() {
+async function readStdinJson(options = {}) {
+  const { timeoutMs = 5000 } = options;
+
   return new Promise((resolve, reject) => {
     let data = '';
+    let settled = false;
+
+    const timer = setTimeout(() => {
+      if (!settled) {
+        settled = true;
+        // Resolve with whatever we have so far rather than hanging
+        try {
+          resolve(data.trim() ? JSON.parse(data) : {});
+        } catch {
+          resolve({});
+        }
+      }
+    }, timeoutMs);
 
     process.stdin.setEncoding('utf8');
     process.stdin.on('data', chunk => {
@@ -198,18 +227,22 @@ async function readStdinJson() {
     });
 
     process.stdin.on('end', () => {
+      if (settled) return;
+      settled = true;
+      clearTimeout(timer);
       try {
-        if (data.trim()) {
-          resolve(JSON.parse(data));
-        } else {
-          resolve({});
-        }
+        resolve(data.trim() ? JSON.parse(data) : {});
       } catch (err) {
         reject(err);
       }
     });
 
-    process.stdin.on('error', reject);
+    process.stdin.on('error', err => {
+      if (settled) return;
+      settled = true;
+      clearTimeout(timer);
+      reject(err);
+    });
   });
 }
 
@@ -313,7 +346,10 @@ function isGitRepo() {
 }
 
 /**
- * Get git modified files
+ * Get git modified files, optionally filtered by regex patterns
+ * @param {string[]} patterns - Array of regex pattern strings to filter files.
+ *   Invalid patterns are silently skipped.
+ * @returns {string[]} Array of modified file paths
  */
 function getGitModifiedFiles(patterns = []) {
   if (!isGitRepo()) return [];
@@ -324,12 +360,18 @@ function getGitModifiedFiles(patterns = []) {
   let files = result.output.split('\n').filter(Boolean);
 
   if (patterns.length > 0) {
-    files = files.filter(file => {
-      return patterns.some(pattern => {
-        const regex = new RegExp(pattern);
-        return regex.test(file);
-      });
-    });
+    // Pre-compile patterns, skipping invalid ones
+    const compiled = [];
+    for (const pattern of patterns) {
+      try {
+        compiled.push(new RegExp(pattern));
+      } catch {
+        // Skip invalid regex patterns
+      }
+    }
+    if (compiled.length > 0) {
+      files = files.filter(file => compiled.some(regex => regex.test(file)));
+    }
   }
 
   return files;
@@ -349,12 +391,23 @@ function replaceInFile(filePath, search, replace) {
 
 /**
  * Count occurrences of a pattern in a file
+ * @param {string} filePath - Path to the file
+ * @param {string|RegExp} pattern - Pattern to count. Strings are treated as
+ *   global regex patterns. RegExp instances are used as-is but the global
+ *   flag is enforced to ensure correct counting.
+ * @returns {number} Number of matches found
  */
 function countInFile(filePath, pattern) {
   const content = readFile(filePath);
   if (content === null) return 0;
 
-  const regex = pattern instanceof RegExp ? pattern : new RegExp(pattern, 'g');
+  let regex;
+  if (pattern instanceof RegExp) {
+    // Ensure global flag is set for correct counting
+    regex = pattern.global ? pattern : new RegExp(pattern.source, pattern.flags + 'g');
+  } else {
+    regex = new RegExp(pattern, 'g');
+  }
   const matches = content.match(regex);
   return matches ? matches.length : 0;
 }