chore: upgrade deps

[ivan-aksamentov]

No description provided.

[Copilot]

Pull Request Overview

This PR upgrades multiple dependencies across the project to their latest versions, focusing on updating commonly used crates like serde, clap, chrono, and other core dependencies.

• Updates serde ecosystem packages (serde, serde_json, serde_stacker) to newer versions
• Upgrades CLI-related dependencies (clap, clap_complete) and other utility crates
• Maintains exact version pinning strategy with "=" prefix for all dependencies

Reviewed Changes

Copilot reviewed 2 out of 3 changed files in this pull request and generated no comments.

File	Description
packages/phyloxml/Cargo.toml	Updates serde and serde_json versions in the phyloxml package
Cargo.toml	Updates multiple dependencies including chrono, clap, indexmap, time, and comfy-table

---

_{Tip: Customize your code reviews with copilot-instructions.md. Create the file or learn how to get started.}