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/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 {