CRITICAL FIX: Fix subshell array corruption in domain discovery

ISSUE:
Pipe-to-while loops created subshells, preventing seen_domains array updates
from persisting to parent shell. This caused:
1. Duplicate domains in reference database
2. Database corruption
3. Inefficient double processing of domains

FIXES:

1. Lines 416-444: Changed pipe-based while to here-document
   - BEFORE: get_user_domains "$user" | while IFS= read -r domain; do
   - AFTER: while IFS= read -r domain; do ... done <<< "$user_domains"
   - Result: seen_domains updates now persist to parent shell

2. Lines 416-417: Call get_user_domains() only once
   - BEFORE: Called twice (lines 417 and 420)
   - AFTER: Called once, stored in $user_domains
   - Result: No duplicate function calls

3. Line 422: Added check for empty primary_domain
   - BEFORE: [ "$domain" = "$primary_domain" ]
   - AFTER: [ -n "$primary_domain" ] && [ "$domain" = "$primary_domain" ]
   - Result: Handles edge case where user has no domains

4. Lines 405-412: Fixed alias iteration subshell issue
   - BEFORE: echo ... | tr ... | while IFS= read -r alias; do
   - AFTER: while IFS= read -r alias; do ... done <<< "$(echo ... | tr ...)"
   - Result: seen_domains["alias"] updates persist

TESTING:
- bash -n validates syntax
- Logic verified for subshell fix
- Array updates will now persist to parent shell

Impact:
- Reference database no longer corrupted with duplicates
- Proper domain deduplication via seen_domains array
- Database building now works correctly

Co-Authored-By: Claude Haiku 4.5 <noreply@anthropic.com>

lib/reference-db.sh

@@ -402,27 +402,32 @@ build_domains_section() {
                 # Also add aliases as separate entries
                 if [ -n "$server_alias" ]; then
                     # Convert space-separated aliases to newline-separated for safe iteration
-                    echo "$server_alias" | tr ' ' '\n' | while IFS= read -r alias; do
+                    # Use here-document instead of pipe to avoid subshell
+                    while IFS= read -r alias; do
                         [ -z "$alias" ] && continue
                         [ -n "${seen_domains[$alias]:-}" ] && continue
 
                         # Alias points to same document root and logs (inherit status from parent)
                         echo "DOMAIN|$alias|$user|$doc_root|$log_path|$php_version|no|alias|$domain|$http_code|$https_code|alias_of_$status_summary" >> "$SYSREF_DB"
                         seen_domains["$alias"]=1
-                    done
+                    done <<< "$(echo "$server_alias" | tr ' ' '\n')"
                 fi
             done
         else
             # Fallback for non-cPanel or if userdata not available
-            local primary_domain=$(get_user_domains "$user" | head -1)
+            local user_domains=$(get_user_domains "$user")
+            local primary_domain=$(echo "$user_domains" | head -1)
 
-            # Use while read to safely iterate over domains (handles spaces)
+            # Use here-document instead of pipe to avoid subshell (allows seen_domains updates to persist)
-            get_user_domains "$user" | while IFS= read -r domain; do
+            while IFS= read -r domain; do
                 [ -z "$domain" ] && continue
                 [ -n "${seen_domains[$domain]:-}" ] && continue
 
                 local is_primary="no"
-                [ "$domain" = "$primary_domain" ] && is_primary="yes"
+                # Only mark as primary if primary_domain is not empty AND matches
+                if [ -n "$primary_domain" ] && [ "$domain" = "$primary_domain" ]; then
+                    is_primary="yes"
+                fi
 
                 # Find log path
                 local log_path="${SYS_LOG_DIR}/${domain}"
@@ -437,7 +442,7 @@ build_domains_section() {
                 # Simple format for non-cPanel (with status codes)
                 echo "DOMAIN|$domain|$user||$log_path||$is_primary|local||$http_code|$https_code|$status_summary" >> "$SYSREF_DB"
                 seen_domains["$domain"]=1
-            done
+            done <<< "$user_domains"
         fi
     done