Remove Makefile and replace make commands

[adamtheturtle]

Summary

• Remove Makefile
• Replace make docs, make open-docs, and make update-secrets commands with direct equivalents

Changes

• Deleted Makefile
• Updated docs/source/contributing.rst to use direct sphinx-build and python commands
• Updated docs/source/ci-setup.rst to use direct tar and gpg commands for updating secrets
• Updated admin/create_secrets_files.py to document the update-secrets commands

Test plan

• Documentation builds correctly with the new commands
• Secret archive update process works with the new commands
• All existing functionality is preserved