Refactor file paths in Makefile, run_script.sh, and start.sh

Update default_env.json to include CLOUDFLARE_CNAME configuration
Update update_dns.py to handle CNAME records for multiple A records
Add .gitignore for env.json in init directory

init/.gitignore

@@ -0,0 +1 @@
+env.json

init/default_env.json

@@ -6,7 +6,9 @@
         "@": true
     },
     "CLOUDFLARE_CNAME": {
-        "*": true
+        "*": {
+            "@": true
+        }
     },
     "CLOUDFLARE_MX": {}
 }