diff --git a/Makefile b/Makefile
index 162775b5fce..c948bd29966 100644
--- a/Makefile
+++ b/Makefile
@@ -342,6 +342,11 @@ lint-errors:
 	@echo "Running error message quality linter..."
 	@go run scripts/lint_error_messages.go
 
+# Check file sizes and function counts
+.PHONY: check-file-sizes
+check-file-sizes:
+	@bash scripts/check-file-sizes.sh
+
 # Validate all project files
 .PHONY: lint
 lint: fmt-check fmt-check-json lint-cjs golint
diff --git a/scripts/check-file-sizes.sh b/scripts/check-file-sizes.sh
new file mode 100755
index 00000000000..4972025cc33
--- /dev/null
+++ b/scripts/check-file-sizes.sh
@@ -0,0 +1,86 @@
+#!/bin/bash
+# check-file-sizes.sh - Monitor Go file sizes and function counts
+#
+# This script identifies Go files that exceed recommended thresholds:
+# - 50+ functions: Consider splitting (warning)
+# - 40-49 functions: Approaching threshold (info)
+#
+# Exit codes:
+#   0 - No issues or only informational warnings
+#   Non-zero is never returned (non-blocking check)
+
+set -euo pipefail
+
+# Colors for output
+RED='\033[0;31m'
+YELLOW='\033[1;33m'
+BLUE='\033[0;34m'
+GREEN='\033[0;32m'
+NC='\033[0m' # No Color
+
+# Thresholds
+WARN_THRESHOLD=50
+INFO_THRESHOLD=40
+
+# Counter for warnings
+warn_count=0
+info_count=0
+
+echo "Checking Go file sizes in pkg/ directory..."
+echo ""
+
+# Find all .go files (excluding test files) and count functions
+while IFS= read -r file; do
+    # Count function declarations (lines starting with "func ")
+    func_count=$(grep -c "^func " "$file" || true)
+    line_count=$(wc -l < "$file")
+    
+    # Only report files with 40+ functions
+    if [ "$func_count" -ge "$WARN_THRESHOLD" ]; then
+        echo -e "${RED}⚠️  WARNING${NC}: $file"
+        echo -e "   Functions: ${RED}$func_count${NC} | Lines: $line_count"
+        echo -e "   Consider splitting this file (threshold: ${WARN_THRESHOLD} functions)"
+        echo ""
+        warn_count=$((warn_count + 1))
+    elif [ "$func_count" -ge "$INFO_THRESHOLD" ]; then
+        echo -e "${YELLOW}ℹ️  INFO${NC}: $file"
+        echo -e "   Functions: ${YELLOW}$func_count${NC} | Lines: $line_count"
+        echo -e "   Approaching threshold (${INFO_THRESHOLD}-${WARN_THRESHOLD} functions)"
+        echo ""
+        info_count=$((info_count + 1))
+    fi
+done < <(find pkg -name "*.go" ! -name "*_test.go" -type f | sort)
+
+# Summary
+echo "━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━"
+echo "Summary:"
+echo ""
+
+if [ "$warn_count" -eq 0 ] && [ "$info_count" -eq 0 ]; then
+    echo -e "${GREEN}✓ All files are within recommended size guidelines${NC}"
+    echo ""
+    echo "No files exceed the 40-function threshold."
+elif [ "$warn_count" -eq 0 ]; then
+    echo -e "${BLUE}ℹ️  $info_count file(s) approaching threshold (${INFO_THRESHOLD}-${WARN_THRESHOLD} functions)${NC}"
+    echo ""
+    echo "These files are getting large but still within acceptable range."
+    echo "Consider reviewing them if adding significant functionality."
+else
+    echo -e "${YELLOW}⚠️  $warn_count file(s) exceed recommended size (${WARN_THRESHOLD}+ functions)${NC}"
+    if [ "$info_count" -gt 0 ]; then
+        echo -e "${BLUE}ℹ️  $info_count file(s) approaching threshold (${INFO_THRESHOLD}-${WARN_THRESHOLD} functions)${NC}"
+    fi
+    echo ""
+    echo "Files exceeding ${WARN_THRESHOLD} functions should be evaluated for splitting."
+    echo "However, domain complexity may justify larger files."
+    echo ""
+    echo "See specs/code-organization.md for file size guidelines and justified large files."
+fi
+
+echo "━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━"
+echo ""
+echo "Note: This is an informational check only. Large files may be justified"
+echo "by domain complexity. See specs/code-organization.md for guidelines."
+
+# Always exit 0 (non-blocking)
+exit 0
diff --git a/specs/code-organization.md b/specs/code-organization.md
index 5507ce987b5..ca4a96eb078 100644
--- a/specs/code-organization.md
+++ b/specs/code-organization.md
@@ -194,6 +194,23 @@ When implementing a feature:
 
 ## File Size Guidelines
 
+### Function Count Threshold
+
+**Guideline**: Consider splitting files when they exceed **50 functions**.
+
+**Note**: This is a guideline, not a hard rule. Domain complexity may justify larger files.
+
+**Monitoring**: Run `make check-file-sizes` to identify files approaching the 50-function threshold.
+
+### Current Large Files
+
+The following files are justified despite their size due to domain complexity:
+
+- `js.go` (41 functions, 914 lines) - JavaScript bundling and execution with many embed directives
+- `permissions.go` (37 functions, 945 lines) - Permission handling with many GitHub Actions permission types
+- `scripts.go` (37 functions, 397 lines) - Script generation with specialized functions for workflow steps
+- `compiler_safe_outputs_consolidated.go` (30 functions, 1267 lines) - Consolidated safe output handling
+
 ### Recommended Sizes
 
 - **Small files**: 50-200 lines