What does this PR do?

This PR fixes the Nix experience, especially when overriding the package.

Related Issue

Fixes #4594

Type of Change

• 🐛 Bug fix (non-breaking change that fixes an issue)
• ✨ New feature (non-breaking change that adds functionality)
• 🔒 Security fix
• 📝 Documentation update
• ✅ Tests (adding or improving test coverage)
• ♻️ Refactor (no behavior change)
• 🎯 New skill (bundled or hub)

Changes Made

• The package now takes dependency-groups as a parameter for more flexible builds.
• Moved the main Hermes Agent package definition from nix/packages.nix to a new, modularized nix/hermes-agent.nix, improving maintainability and reusability.
• The package now takes dependency-groups as a parameter for more flexible builds.
• Added nix/overlays.nix, providing a Nix overlay that exposes the Hermes Agent package for easier consumption in external Nix projects.
• Add uv2nix override for matrix-nio

How to Test

1. Set up hermes-agent on NixOS by following our documentation
2. Add matrix as messaging platform, and switch to the new generation will fall into [Setup]: Matrix does not work on NixOS setup #4594
3. Override the package as follows to make it work:

   nixpkgs = {
     overlays = [ inputs.hermes-agent.overlays.default ];
     config.permittedInsecurePackages = [ "olm-3.2.16" ];
   };
   
   services.hermes-agent = {
     enable = true;
     package = pkgs.hermes-agent.override {
       dependency-groups = [ "matrix" ];
     };
   };

Checklist

Code

• I've read the Contributing Guide
• My commit messages follow Conventional Commits (fix(scope):, feat(scope):, etc.)
• I searched for existing PRs to make sure this isn't a duplicate
• My PR contains only changes related to this fix/feature (no unrelated commits)
• I've run pytest tests/ -q and all tests pass
• I've added tests for my changes (required for bug fixes, strongly encouraged for features)
• I've tested on my platform: x86_64-linux, NixOS with nixpkgs-unstable

Documentation & Housekeeping

• I've updated relevant documentation (README, docs/, docstrings) — or N/A
• I've updated cli-config.yaml.example if I added/changed config keys — or N/A
• I've updated CONTRIBUTING.md or AGENTS.md if I changed architecture or workflows — or N/A
• I've considered cross-platform impact (Windows, macOS) per the compatibility guide — or N/A
• I've updated tool descriptions/schemas if I changed tool behavior — or N/A

For New Skills

• This skill is broadly useful to most users (if bundled) — see Contributing Guide
• SKILL.md follows the standard format (frontmatter, trigger conditions, steps, pitfalls)
• No external dependencies that aren't already available (prefer stdlib, curl, existing Hermes tools)
• I've tested the skill end-to-end: hermes --toolsets skills -q "Use the X skill to do Y"

Screenshots / Logs