Claude Code Configuration Manager Skill

Claude Code Configuration Manager

Overview

This system uses a declarative Nix home-manager module (programs.claude-code) to manage all Claude Code configuration. Files under ~/.claude/ are Nix-managed symlinks to the Nix store and must NOT be edited directly.

Architecture

Two modules work together:

programs.claude-code (upstream home-manager) — settings, skills, agents, commands, hooks, mcpServers, memory (CLAUDE.md), rules
programs.claude-code-nix (our custom module) — LSP servers with Nix store paths, statusline scripts, shell aliases, extra packages

flake.nix
  └─ modules/home-manager/default.nix    # Option VALUES for both modules
       ├─ programs.claude-code (upstream)
       │    └─ Generates: ~/.claude/settings.json
       │                  ~/.claude/CLAUDE.md
       │                  ~/.claude/skills/*/
       │                  ~/.claude/agents/
       │                  ~/.claude/commands/
       └─ programs.claude-code-nix (our module: claude-code.nix)
            └─ Generates: ~/.claude/statusline-command.sh
                          ~/.claude/custom-plugins/lsp-servers/.lsp.json
                          Shell aliases (claude, clod)

Key Files

| File | Purpose | |------|---------| | modules/home-manager/claude-code.nix | Our Nix extensions module (LSP, statusline, aliases) | | modules/home-manager/default.nix | Where ALL option values are set | | modules/home-manager/packages/claude-code.nix | Claude Code binary package derivation | | flake.nix | System composition — extraHomeManagerModules for per-device overrides | | systems/work/claude-code.nix | Work laptop override template | | skills/ | Custom skill sources (home-assistant, llm-orchestrator, claude-code-config) | | agents/ | Sub-agent definitions for multi-model review | | commands/ | Custom command definitions |

How To: Common Operations

Add an MCP Server

In modules/home-manager/default.nix, add to programs.claude-code.mcpServers:

programs.claude-code.mcpServers.my-server = {
  command = "mcp-server-my-thing";
  args = [ "--flag" "value" ];
  env = { MY_VAR = "value"; };
};

Then rebuild: nixswitch

Add an LSP Server

In modules/home-manager/default.nix, add to programs.claude-code-nix.lsp.servers:

programs.claude-code-nix.lsp.servers.rust = {
  command = "${pkgs.rust-analyzer}/bin/rust-analyzer";
  args = [ ];
  extensionToLanguage = { ".rs" = "rust"; };
};

Always use absolute Nix store paths (${pkgs.foo}/bin/foo) for the command.

Add a Permission

In modules/home-manager/default.nix, add to programs.claude-code.settings.permissions.allow:

programs.claude-code.settings.permissions.allow = [
  # ... existing permissions ...
  "Bash(my-new-command:*)"
];

Add a Skill

Create the skill directory at skills/<skill-name>/SKILL.md
In modules/home-manager/default.nix, add to programs.claude-code.skills:

programs.claude-code.skills.my-skill = ./../../skills/my-skill;

Skills can be directories (with SKILL.md inside) or inline strings.

Disable a Skill on a Specific Device

In a per-device override module (e.g., systems/work/claude-code.nix):

programs.claude-code.skills.home-assistant = lib.mkForce "";

Add Hooks

In modules/home-manager/default.nix:

programs.claude-code.settings.hooks = {
  PreToolUse = [
    {
      type = "command";
      command = "my-hook-script";
      matcher = "Bash(rm *)";
    }
  ];
};

Override Config for Work Device

Edit systems/work/claude-code.nix with work-specific overrides
In flake.nix, add it to the work system's extraHomeManagerModules:

darwinConfigurations."work-macbook" = mkDarwinConfig {
  username = "cullen";
  system = "aarch64-darwin";
  hostname = "work-macbook";
  extraHomeManagerModules = [ ./systems/work/claude-code.nix ];
};

The Nix module system merges lists (permissions), attrsets (MCP servers, LSP, skills), and strings (memory) automatically.

Update Claude Code Package Version

In modules/home-manager/packages/claude-code.nix, update the version and platformHashes. Or override via the module:

programs.claude-code.package = pkgs.callPackage ./packages/claude-code.nix {
  version = "2.2.0";
  platformHashes = { ... };
};

Search for Marketplace Skills

Use WebFetch to browse the Claude Code plugin marketplace:

Marketplace: https://api.anthropic.com/mcp-registry/docs
Official skills repo: https://github.com/anthropics/skills

Look Up Latest Claude Code Docs

Fetch these URLs for up-to-date documentation:

Settings: https://docs.anthropic.com/en/docs/claude-code/settings
Plugins: https://docs.anthropic.com/en/docs/claude-code/plugins
Hooks: https://docs.anthropic.com/en/docs/claude-code/hooks
Skills: https://docs.anthropic.com/en/docs/claude-code/skills
MCP: https://docs.anthropic.com/en/docs/claude-code/mcp

Anti-Patterns (Do NOT Do These)

Never edit ~/.claude/settings.json directly — it's a read-only Nix symlink. Use programs.claude-code.settings.* options instead.
Never run claude plugins install for LSP plugins — LSP is Nix-managed via programs.claude-code-nix.lsp.servers. Marketplace LSP plugins will conflict.
Never create files in ~/.claude/ manually — use the module options. Manual files will be orphaned or overwritten by home-manager.
Never use bare command names in LSP config — always use ${pkgs.foo}/bin/foo absolute paths to avoid PATH resolution issues.
Never add skills/agents/commands directly to ~/.claude/ — add them to the skills/, agents/, or commands/ directories in the repo and wire them through the module.

Module Options Reference

`programs.claude-code` (upstream home-manager)

| Option | Type | Description | |--------|------|-------------| | enable | bool | Enable Claude Code | | package | package | The claude-code package | | settings | JSON attrs | Flat JSON merged into settings.json | | mcpServers | attrs | MCP server definitions (wrapped into binary) | | memory.text | str | CLAUDE.md content | | skills | attrs of (str or path) | Skills (dirs or inline SKILL.md content) | | agents / agentsDir | attrs or path | Agent definitions | | commands / commandsDir | attrs or path | Command definitions | | hooks / hooksDir | attrs or path | Hook scripts | | rules / rulesDir | attrs or path | Rule files | | outputStyles | attrs | Output style files |

`programs.claude-code-nix` (our Nix extensions)

| Option | Type | Description | |--------|------|-------------| | enable | bool | Enable Nix extensions | | lsp.enable | bool | Enable LSP plugin | | lsp.servers | attrs | LSP servers with absolute Nix store paths | | statusLine.enable | bool | Enable custom statusline | | statusLine.scriptText | null or str | Custom script (null = default 3-line) | | extraPackages | list of package | Additional packages |

Agent Skills: Claude Code Configuration Manager

Install this agent skill to your local

Skill Files