Refactor: remove redundant PHP_MODULE entries in several scripts

[MickLesk]

✍️ Description

• Add dom and gmp to BASE_MODULES in setup_php()
• Remove modules already covered by BASE_MODULES (cli,common,bcmath,curl,dom,gd,gmp,intl,mbstring,readline,xml,zip)
• Remove modules already covered by EXTENDED_MODULES (mysql,sqlite3,pgsql,redis,imagick,bz2,apcu)
• Remove modules already covered by BUILTIN (ctype,exif,ffi,fileinfo,gettext,iconv,pdo,tokenizer)

🔗 Related Issue

Fixes #

✅ Prerequisites (X in brackets)

• Self-review completed – Code follows project standards.
• Tested thoroughly – Changes work as expected.
• No security risks – No hardcoded secrets, unnecessary privilege escalations, or permission issues.

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🛠️ Type of Change (X in brackets)

• 🐞 Bug fix – Resolves an issue without breaking functionality.
• ✨ New feature – Adds new, non-breaking functionality.
• 💥 Breaking change – Alters existing functionality in a way that may require updates.
• 🆕 New script – A fully functional and tested script or script set.
• 🌍 Website update – Changes to website-related JSON files or metadata.
• 🔧 Refactoring / Code Cleanup – Improves readability or maintainability without changing functionality.
• 📝 Documentation update – Changes to README, AppName.md, CONTRIBUTING.md, or other docs.