Add Codex integration: CLI support, project config generation, and docs

[sergiobaiao]

Motivation

• Add support for Codex as a first-class project-local integration so users can configure OpenPets for Codex MCP usage.
• Provide documentation and a validation guide to help users configure and verify Codex integration locally.
• Extend CLI project-configuration tooling to consistently emit Codex MCP entries with secure file handling.

Description

• Added Codex documentation at docs/codex-integration.md and linked it from README.md with usage examples and expected .codex/config.toml output.
• Updated README.md to include codex in the integrations list and reference the new docs page.
• Introduced docs/repository-analysis.md describing repository architecture, risks, and recommended deep dives.
• Extended CLI parsing and help text in packages/cli/src/index.ts to accept --agent codex and implemented configureCodexProject, writeCodexProjectConfig, and TOML construction helpers to atomically write .codex/config.toml with secure permissions.
• Updated packages/cli/src/check-cli-contract.ts to include automated contract tests for the codex configure flow and related behaviors.

Testing

• Ran the CLI contract validation script in packages/cli/src/check-cli-contract.ts, which exercised parsing, project configuration flows (including Codex), and help output assertions, and it completed with the contract validation message indicating success.
• The codex configure path was validated by assertions that .codex/config.toml contains an [mcp_servers.openpets] block and that the --local-dev --force variations produce a node-based command entry, and those assertions passed.

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Codex Task

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