Reference Map

This page answers two questions:

where do I change X?
what file actually drives it?

Paths are relative to the repo root. Hooks live under home/.chezmoiscripts/ and run in numeric order; helper scripts live under scripts/.

Chezmoi

Component	Source path
Prompts / data	`home/.chezmoi.toml.tmpl`
Shared data	`home/.chezmoidata/`
Externals	`home/.chezmoiexternal.toml`
Ignore rules	`home/.chezmoiignore`
Hooks	`home/.chezmoiscripts/`

Provisioning hooks (first run)

Hook	Source path
Xcode CLT	`run_once_before_00-install-xcode.sh`
Homebrew install	`run_once_after_01-install-brew.sh`
Fish install + login shell	`run_once_after_02-install-fish.sh`
Pass managers setup	`run_once_after_05-setup-pass-managers.fish.tmpl`

Packages

Each registry has a declarative list plus the hook that converges it. See Packages.

Registry	List source	Converge hook
Homebrew	`home/.chezmoitemplates/brews/` (per-category, per-profile partials assembled into `home/readonly_dot_Brewfile.tmpl`)	`run_onchange_after_03-install-brew-packages.fish.tmpl`
Fish plugins	`home/dot_config/fish/readonly_fish_plugins`	`run_onchange_after_04-update-fish-packages.fish.tmpl`
mise runtimes	`home/dot_config/mise/config.toml.tmpl`	`run_onchange_after_05-install-mise-runtimes.sh.tmpl`
Cargo crates	`home/readonly_dot_default-cargo-crates`	`run_onchange_after_05-update-cargo-crates.sh.tmpl`
Go tools	`home/readonly_dot_default-golang-pkgs.tmpl`	`run_onchange_after_05-update-golang-pkgs.sh.tmpl`
Ruby gems	`home/readonly_dot_default-gems`	`run_onchange_after_05-update-gems.sh.tmpl`
Global yarn	`home/readonly_dot_default-yarn-pkgs`	`run_onchange_after_05-update-yarn-pkgs.sh.tmpl`
uv python versions	`home/readonly_dot_python-version`	`run_onchange_after_05-install-uv-versions.sh.tmpl`
uv tools	`home/readonly_dot_default-uv-tools.tmpl`	`run_onchange_after_06-update-uv-tools.sh.tmpl`
Custom packages	`home/readonly_dot_default-custom-packages.tmpl`	`run_onchange_after_05-install-custom-packages.sh.tmpl`
GitHub CLI extensions	(declared in hook)	`run_onchange_after_05-install-gh-extensions.fish.tmpl`
llama.cpp GGUF models	`home/readonly_dot_default-llama-cpp-models.tmpl`	`run_onchange_after_07-sync-llama-cpp-models.sh.tmpl`

Shell

Component	Source path
Fish main config	`home/dot_config/fish/readonly_config.fish.tmpl`
POSIX shellrc (alias)	`home/readonly_dot_shellrc`
Zsh completions	`home/dot_zsh/`
Starship prompt	`home/dot_config/readonly_starship.toml`
Shared ignores (fd/fzf)	`home/dot_config/readonly_ignore-globs`

Git + Identity

Component	Source path
Git main config template	`home/private_readonly_dot_gitconfig.tmpl`
Work override gitconfig	`home/work/private_dot_gitconfig.tmpl`
SSH config (1Password agent socket)	`home/private_dot_ssh/private_executable_config`
Allowed signers (SSH signing)	`home/private_dot_ssh/private_executable_allowed_signers.tmpl`
1Password SSH agent config	`home/dot_config/exact_private_1Password/exact_ssh/readonly_agent.toml.tmpl`
gh picker work config	`home/dot_config/exact_tmux/exact_scripts/pickers/github/readonly_gh-picker-work.yml`
gh picker home config	`home/dot_config/exact_tmux/exact_scripts/pickers/github/readonly_gh-picker-home.yml`

Editor

Component	Source path
Neovim	`home/dot_config/exact_nvim/`

Terminal + Multiplexing

Component	Source path
tmux	`home/dot_config/exact_tmux/readonly_tmux.conf`
Ghostty	`home/dot_config/exact_ghostty/readonly_config`
bat	`home/dot_config/exact_bat/readonly_config`
Yazi (file mgr)	`home/dot_config/yazi/`
lazygit	`home/dot_config/exact_lazygit/config.yml`
gitui	`home/dot_config/exact_gitui/`
tig	`home/dot_config/exact_tig/readonly_config`
btop	`home/dot_config/exact_btop/btop.conf`
gh-dash	`home/dot_config/exact_gh-dash/`

macOS Automation

Component	Source path
Defaults scripts	`home/.osx.core`, `home/.osx.extra`
Defaults hooks	`run_onchange_after_05-osx.core.sh.tmpl`, `...05-osx.extra...`
Hammerspoon	`home/dot_hammerspoon/`
Karabiner	`home/dot_config/exact_private_karabiner/`
App icons mapping	`home/app_icons/readonly_icon_mapping.yaml`
App icons hook	`run_onchange_after_05-apply-app-icons.sh.tmpl`
Crontab	`run_onchange_after_05-install-crontab.sh.tmpl`

AI: governance + skills

See The Agentic Operating System.

Component	Source path
Assistant SOP (single source)	`home/readonly_AGENTS.md` (`~/CLAUDE.md`, `~/.gemini/GEMINI.md`, `~/.cursor/AGENTS.md`, `~/.config/opencode/AGENTS.md` are symlinks to `~/AGENTS.md`)
Assistant skills	`home/exact_dot_agents/exact_skills/`
Cursor CLI hooks	`home/dot_cursor/hooks.json`, `home/exact_dot_agents/exact_hooks/`

AI: harness configs

Per-tool config sources and the run_onchange_after_07-* hooks that render them. See Tool configs.

Tool	Source	Merge hook
Claude Code	`home/dot_claude/`	`run_onchange_after_07-merge-claude-code-settings.sh.tmpl`
Codex	`home/dot_codex/`	`run_onchange_after_07-merge-codex-config.sh.tmpl`
Gemini	`home/dot_gemini/`	`run_onchange_after_07-merge-gemini-settings.sh.tmpl`
OpenCode	`home/dot_config/opencode/`	`run_onchange_after_07-merge-opencode-config.sh.tmpl`
Pi	`home/dot_pi/agent/`	`run_onchange_after_07-merge-pi-config.sh.tmpl`
Cursor	`home/dot_cursor/`	(settings tracked directly)
Amp	`home/dot_config/exact_amp/`	(settings tracked directly)

AI: model registry

Single source of truth for LiteLLM/Azure model definitions; per-tool model configs are generated from it. See Model registry & routing.

Component	Source path
Model definitions	`home/.chezmoidata/ai_models.yaml`
YAML reader	`scripts/ai_models.py`
Pi models generator	`scripts/generate_pi_models.py`
OpenCode models merge	`scripts/merge_opencode_models.py`
Display-name formatting	`scripts/model_display.py`
Prompt-cache probe	`scripts/probe_litellm_prompt_cache.py`

AI: MCP

Canonical MCP registry plus the generator/injectors that fan it out per tool. See MCP servers.

Component	Source path
MCP registry	`home/.chezmoidata/mcp_servers.yaml`
Registry reader	`scripts/mcp_registry.py`
Config generator	`scripts/generate_mcp_configs.py`
Codex injector	`scripts/inject_mcp_into_codex_toml.py`
OpenCode injector	`scripts/inject_mcp_into_opencode_jsonc.py`
Claude MCP merge	`scripts/merge_claude_mcp.py`
Generate hook	`run_onchange_after_07-generate-mcp-configs.sh.tmpl`

AI: memory

Two distinct memory layers. See Agent memory.

Component	Source path
AI knowledge base (`,ai-kb`)	`home/exact_bin/executable_,ai-kb`, `scripts/ai_kb.py`
Embedding service	`scripts/embed.py`, `scripts/embed_runner.py`
Vector retrieval	`scripts/vec_runner.py`
Hook memory (`,agent-memory`)	`home/exact_bin/executable_,agent-memory`, `scripts/agent_memory.py`

AI: Ralph orchestrator

See Ralph orchestrator.

Component	Source path
CLI entry	`home/exact_bin/executable_,ralph`
Orchestrator	`scripts/ralph.py`
Roles + diversity	`home/dot_config/ralph/roles.json`
Role prompts	`home/dot_config/ralph/prompts/`
Dashboard (TUI)	`tools/ralph-tui/`
TUI build hook	`run_onchange_after_06-build-ralph-tui.sh.tmpl`

AI: local inference

See llama.cpp local inference.

Component	Source path
GGUF model manifest	`home/readonly_dot_default-llama-cpp-models.tmpl`
Router preset (INI)	`home/dot_config/llama.cpp/models.ini.tmpl`
Chat template	`home/dot_config/llama.cpp/readonly_qwen3.6-chat-template.jinja` (robust Unsloth template; `local-max` override for system-message ordering)
Sync hook + helper	`run_onchange_after_07-sync-llama-cpp-models.sh.tmpl`, `scripts/sync_llama_cpp_models.py`
Control plane	`home/exact_bin/executable_,llama-cpp`
Claude launcher	`home/exact_bin/executable_,claude-llama-cpp`
Codex launcher	`home/exact_bin/executable_,codex-llama-cpp`, catalog shim `home/exact_bin/executable_codex`
OpenCode launcher	`home/exact_bin/executable_,opencode-llama-cpp` (provider in `opencode.personal.jsonc` / `opencode.work.jsonc`)
Pi provider	`home/dot_pi/agent/readonly_models.json` (`local` + `local-max`)

Scripts (`scripts/`)

Helper scripts called by hooks and commands (stdlib-only by convention).

Script	Purpose
`chezmoi_lib.sh`	Shared shell library for merge/apply hooks (source selection, atomic writes, checksums, LiteLLM base)
`verify_templates.py`	Render every chezmoi `*.tmpl` via `execute-template` to catch errors early
`verify_mermaids.py`	Check `.mermaids/` file-census counts against `git ls-files` (part of `make check`)
`yaml_parser.py`	Minimal dependency-free YAML parser for project data files
`jsonc_dump.py`	JSONC serializer matching OpenCode's trailing-comma config style
`mcp_registry.py`	Read/normalize the canonical MCP registry
`generate_mcp_configs.py`	Generate tool-specific MCP configs from `mcp_servers.yaml`
`inject_mcp_into_codex_toml.py`	Inject MCP servers into Codex TOML at a marker line
`inject_mcp_into_opencode_jsonc.py`	Inject MCP servers into an OpenCode JSONC placeholder
`merge_claude_mcp.py`	Surgically update only `mcpServers` in `~/.claude.json`
`merge_opencode_models.py`	Merge LiteLLM/Azure models into OpenCode JSONC
`ai_models.py`	Parse the `litellm_models` / `azure_models` sections of `ai_models.yaml`
`generate_pi_models.py`	Build Pi `models.json` from the shared base plus LiteLLM/Azure providers
`model_display.py`	Shared display-name formatting for LiteLLM model entries
`probe_litellm_prompt_cache.py`	Probe prompt-cache signals across LiteLLM models
`ai_kb.py`	Local markdown + SQLite FTS5/vector knowledge base for agent runs
`embed.py`	Stdlib embedding-service abstraction that shells out to `embed_runner.py`
`embed_runner.py`	Isolated PEP 723 `fastembed` runner (`BAAI/bge-small-en-v1.5`, 384-d)
`vec_runner.py`	Isolated PEP 723 `sqlite-vec` KNN/pairs runner for the KB
`agent_memory.py`	Inspect/wipe hook memory under `/tmp/specs` for the current workspace
`ralph.py`	Ralph orchestrator state machine (planner -> executor -> reviewer -> re_reviewer)
`sync_llama_cpp_models.py`	Download missing GGUF files declared in the llama.cpp manifest
`reconcile_golang_pkgs.py`	Reconcile Go binaries against the manifest (hook 05-update-golang-pkgs)
`reconcile_custom_packages.py`	Reconcile source-installed custom package artifacts
`yt_search.py`	YouTube search backend (powers `,youtube-search`)
`tests/`	Python test suite (`test_scripts.py`, agent-hook tests)

Maintenance / cleanup hooks

Idempotent housekeeping that removes orphaned generated state on apply.

Hook	Purpose
`run_onchange_after_08-cleanup-orphaned-agent-skill-dirs.sh.tmpl`	Drop skill dirs no longer in the source tree
`run_onchange_after_08-cleanup-orphaned-ralph-fzf-scaffold.sh.tmpl`	Remove stale Ralph fzf scaffold artifacts
`run_onchange_after_08-cleanup-orphaned-tmux-pick_session.sh.tmpl`	Remove stale tmux `pick_session` artifacts

Formatting

Component	Source path
Format script	`bin/fmt`
EditorConfig	`.editorconfig`
Prettier config	`.prettierrc`
Prettier ignore	`.prettierignore`
StyLua config	`.stylua.toml`
Ruff config	`ruff.toml`

Custom Commands

Component	Source path
Commands source	`home/exact_bin/`

Chezmoi​

Provisioning hooks (first run)​

Packages​

Shell​

Git + Identity​

Editor​

Terminal + Multiplexing​

macOS Automation​

AI: governance + skills​

AI: harness configs​

AI: model registry​

AI: MCP​

AI: memory​

AI: Ralph orchestrator​

AI: local inference​

Scripts (scripts/)​

Maintenance / cleanup hooks​

Formatting​

Custom Commands​