Fix critical bugs found by QA tool: grep -F, integer comparisons, function exports

CRITICAL FIXES (8 → 0):
- Fix all 8 grep -F with regex anchors bugs
  - lib/reference-db.sh:420
  - lib/user-manager.sh:195, 254, 258, 317, 583, 590
  - modules/website/500-error-tracker.sh:313
  - Changed grep -F to grep for proper regex support

HIGH PRIORITY FIXES:
- Add 36 function exports for subshell availability
  - lib/system-detect.sh: 10 functions
  - lib/common-functions.sh: 26 functions

- Fix 27 integer comparisons with ${var:-0} validation
  - lib/common-functions.sh: 7 fixes
  - lib/ip-reputation.sh: 3 fixes
  - lib/user-manager.sh: 4 fixes
  - launcher.sh: 7 fixes
  - modules/website/500-error-tracker.sh: 1 fix
  - modules/performance/hardware-health-check.sh: 2 fixes
  - modules/performance/mysql-query-analyzer.sh: 1 fix
  - modules/security/bot-analyzer.sh: 11 fixes

- Change exit to return in library file
  - lib/common-functions.sh:246 (require_root function)

DOCUMENTATION:
- Add [DEVELOPMENT_WORKFLOW] section to REFDB_FORMAT.txt
  - Document QA script as "third option" for validation
  - Add recommended workflow for using QA tool
  - Document all 16 checks (11 bug + 5 performance)

IMPACT:
- Before: 41 issues (8 CRITICAL + 13 HIGH + 9 MEDIUM + 11 LOW)
- After: 30 issues (0 CRITICAL + 10 HIGH + 9 MEDIUM + 11 LOW)
- 27% reduction, all CRITICAL bugs eliminated

QA Tool: bash /tmp/toolkit-qa-check.sh /root/server-toolkit

modules/performance/mysql-query-analyzer.sh

@@ -292,7 +292,7 @@ run_quick_health_check() {
 
     echo "  Active Connections: $connections / $max_connections (${conn_percent}%)"
 
-    if [ $conn_percent -gt 80 ]; then
+    if [ "${conn_percent:-0}" -gt 80 ]; then
         print_warning "Connection usage is high (${conn_percent}%)"
     fi