Add uv to nix and fix resulting problems

[jeff-hykin]

• Tested on Linux and MacOS with nix develop
• The default uv is too old (conflicts with our pyproject.toml), so needed to update nixpkgs (flake update)
• Flake update causes home manager to break (of a change on nixpkgs unstable), pinning to nixos-25.11 fixes that
• pre-commit depends on dotnet (for some fricken reason) which is broken on unstable and 25.11, so I switched to the last working version of pre-commit
• groups, envVarShellHook, and vars were created to enable debugging the flake from a nix repl (helpful now and in the future)

[greptile-apps]

Greptile Summary

Updated Nix flake to support uv by upgrading to nixpkgs 25.11, which required pinning home-manager to release-25.11 and working around a broken pre-commit package by using a specific older nixpkgs commit (f665af0).

• Migrated from nixos-unstable to nixos-25.11 to get compatible uv version for pyproject.toml requirements
• Pinned home-manager to release-25.11 to fix breaking changes from nixpkgs unstable
• Added workaround for broken pre-commit by sourcing from specific nixpkgs commit where dotnet dependency works
• Refactored package aggregation into groups structure for better organization
• Split shellHook into envVarShellHook and full shellHook for reusability
• Exported vars attribute containing inputs, pkgs, groups, aggregation, and hooks for REPL debugging
• Added Darwin-specific target configuration to fix home-manager app linking issue

Confidence Score: 4/5

• This PR is safe to merge with minimal risk - it's a necessary infrastructure update with well-documented workarounds
• Score reflects the necessary nature of the update to support uv tooling while appropriately handling breaking changes through version pins. The workarounds (pre-commit from older nixpkgs, home-manager pinned to 25.11) are well-justified and documented. The refactoring to groups structure improves code organization without changing functionality. Minor concern: using a specific commit hash for pre-commit is fragile long-term, but acceptable as a temporary fix
• No files require special attention - the changes are straightforward dependency updates and structural improvements

Important Files Changed

Filename	Overview
flake.nix	Updated nixpkgs to 25.11, added uv package, pinned home-manager and pre-commit to working versions, refactored package groups structure for better organization and REPL debugging
flake.lock	Updated lock file with nixpkgs 25.11, home-manager release-25.11, and new nixpkgsSourceWithPreCommit input

Sequence Diagram

sequenceDiagram
    participant Dev as Developer
    participant Flake as flake.nix
    participant Lock as flake.lock
    participant NixPkgs as nixpkgs (25.11)
    participant PreCommit as nixpkgsSourceWithPreCommit
    participant HomeManager as home-manager (25.11)
    
    Dev->>Flake: flake update
    Flake->>NixPkgs: Update from unstable to 25.11
    Flake->>HomeManager: Pin to release-25.11
    Flake->>PreCommit: Add f665af0 commit for working pre-commit
    NixPkgs-->>Lock: Update hashes and commits
    HomeManager-->>Lock: Update to 25.11 release
    PreCommit-->>Lock: Add new input source
    Flake->>Flake: Add uv package
    Flake->>Flake: Refactor to groups structure
    Flake->>Flake: Split shellHook into envVarShellHook
    Flake->>Flake: Export vars for REPL debugging
    Lock-->>Dev: Dependencies resolved

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