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