feat: align CLI identity with Every Code

[shiny-code-bot]

Summary

• align CLI help, examples, and status messages with Every Code and the code command
• make ~/.code/config.toml the primary config path in shared CLI help while preserving legacy ~/.codex compatibility copy
• repair root package scripts for the Codex-base crate/bin names now used under code-rs
• update generated resume hints and exec usage to say code resume / code exec

Validation

• ./build-fast.sh
• help spot checks: code --help, code exec --help, code mcp add --help, code plugin marketplace --help, code app-server --help
• review agents: identity-config-final-review and identity-config-postfix-review

Notes

• Codex Desktop app and Codex Cloud references are intentionally retained in this slice.
• Internal codex-* crate/package names and CODEX_* compatibility names are intentionally retained where they are substrate or external compatibility surfaces.