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Highly-opinionated setup for AI safety research with coding agents

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# dotfiles

**Highly opinionated** development environment for AI safety research. ZSH, Tmux, Vim, SSH, and AI coding assistants across macOS, Linux, and cloud containers.

This setup reflects workflows optimized for ML research: reproducibility, experiment tracking, async API patterns, and rigorous methodology. The AI assistant configurations enforce research discipline—interview before planning, plan before implementing, skepticism of surprisingly good results.

**Key highlights:**

- 🤖 **AI Coding Assistants** - Extensively configured Claude Code, plus Codex CLI, OpenCode, and Antigravity CLI support
- 👻 **[Ghostty](https://ghostty.org/)** - Fast, GPU-accelerated terminal with sensible defaults
- 📊 **[htop](https://htop.dev/)** - Dynamic CPU meter configuration that adapts to your core count
- 🦀 **Rust-powered CLI tools** - Modern, blazing-fast replacements for standard Unix utilities
- 🧹 **Automatic cleanup** - Scheduled cleanup of Downloads/Screenshots (macOS, moves to trash)

> Originally forked from [jplhughes/dotfiles](https://github.com/jplhughes/dotfiles) - thanks John for the solid foundation!

> **AI agents working here:** start with [`CLAUDE.md`](./CLAUDE.md) — top rules, a common-tasks table, and pointers into [`docs/deploy-components.md`](./docs/deploy-components.md) (deploy behavior, cloud, extending) and [`docs/tooling-and-packages.md`](./docs/tooling-and-packages.md) (packages, symlink-vs-copy, gotchas). This README is human-oriented onboarding; CLAUDE.md is the operational doc.

## Quickstart

This project offers two quickstart paths: **Local** and **Cloud**.

---

### Local Quickstart

For setting up on your personal machine (macOS, Linux, desktop/laptop):

```bash
git clone https://github.com/yulonglin/dotfiles.git && cd dotfiles

# 1. Install dependencies (zsh, tmux, CLI tools, AI assistants)
./install.sh

# 2. Deploy configurations (symlinks, shell config, secrets, automation)
./deploy.sh

# 3. Restart your shell
source ~/.zshrc
```

- `install.sh` installs required software.
- `deploy.sh` deploys config files and settings.
- Both scripts are **idempotent** and safe to re-run.

All configuration options are stored in [`config.sh`](./config.sh). Flags are **additive** (e.g., `--mouseless` adds that feature to defaults). Use `--minimal` to disable most options.

---

### Cloud Quickstart

For cloud environments (RunPod, Hetzner, Lambda Labs, etc):

1. **SSH into your new remote machine as root.**
2. **Run the one-liner:**
   ```bash
   # RunPod (fresh pod)
   curl -fsSL https://raw.githubusercontent.com/yulonglin/dotfiles/main/scripts/cloud/setup.sh | bash

# Hetzner / standard VPS (persistent /home)
   curl -fsSL https://raw.githubusercontent.com/yulonglin/dotfiles/main/scripts/cloud/setup.sh | USER_HOME=/home bash
   ```
   This creates a non-root user, installs dependencies, clones dotfiles, and runs `install.sh --profile=cloud` + `deploy.sh --profile=cloud` (a lean remote-dev set — no pueue/zotero/Rust toolchain). It will prompt for GitHub auth.

Provisions the **`main`** branch by default. To pin another branch, pass `--branch` (use `bash -s --` to forward args through `curl | bash`) or set `DOTFILES_BRANCH`:
   ```bash
   curl -fsSL https://raw.githubusercontent.com/yulonglin/dotfiles/main/scripts/cloud/setup.sh | bash -s -- --branch yulong
   ```
3. **Reconnect as your user:**
   ```bash
   ssh yulong@<ip>
   ```
4. **(Optional) After pod restart** (RunPod recreates `/etc/passwd`):
   ```bash
   curl -fsSL https://raw.githubusercontent.com/yulonglin/dotfiles/main/scripts/cloud/restart.sh | bash
   ```
5. **(Optional) Customize components:**
   Edit [`config.sh`](./config.sh) to disable resource-intensive options (AI assistants, cleanup automation, etc.) before running install/deploy.

**Tip:** The setup auto-detects cloud providers and adjusts accordingly (persistent storage paths, SSH config, no macOS-only features). See [`scripts/cloud/README.md`](./scripts/cloud/README.md) for details.

## Table of Contents

- [Quickstart](#quickstart)
- [Adopting These Dotfiles](#adopting-these-dotfiles)
- [Rust CLI Tools](#rust-cli-tools)
- [Installation](#installation)
  - [Step 1: Install dependencies](#step-1-install-dependencies)
  - [Step 2: Deploy configurations](#step-2-deploy-configurations)
- [AI Assistants](#ai-assistants)
  - [Claude Code](#claude-code-primary-ai-assistant)
  - [Codex CLI](#codex-cli-openai)
  - [Antigravity CLI + OpenCode](#antigravity-cli-google--opencode)
- [Terminal & Shell](#terminal--shell)
  - [Ghostty](#ghostty-terminal-emulator)
  - [Powerlevel10k Prompt](#powerlevel10k-prompt)
  - [Claude Code Statusline](#claude-code-statusline)
  - [SSH Key Management](#ssh-key-management)
- [Dev Tools](#dev-tools)
  - [htop](#htop-process-monitor)
  - [pdb++](#pdb-python-debugger)
- [Secrets & Security](#secrets--security)
  - [Encrypted Secrets (Bitwarden Secrets Manager)](#encrypted-secrets-bitwarden-secrets-manager)
  - [Gist Sync](#gist-sync-automation-both-platforms)
  - [Global Git Hooks](#global-git-hooks)
  - [Supply Chain Defense](#supply-chain-defense)
- [Automation](#automation)
  - [Automatic Cleanup](#automatic-cleanup-macos)
  - [Claude Code Session Cleanup](#claude-code-session-cleanup-both-platforms)
  - [AI Tools Auto-Update](#ai-tools-auto-update-both-platforms)
  - [Package Auto-Update](#package-auto-update-both-platforms)
  - [Text Replacements](#text-replacements-macos)
- [Cloud Setup](#cloud-setup-runpod-hetzner-etc)
- [Getting to Know These Dotfiles](#getting-to-know-these-dotfiles)

## Adopting These Dotfiles

This repo is highly personal — it reflects one person's workflow, opinions, and tooling choices. The best way to use it is to **point a coding agent at this repo and ask it to extract the parts you find useful** into your own dotfiles.

**What's generalizable vs personal:**

| Generalizable (worth extracting)                   | Personal (skip or replace)        |
| -------------------------------------------------- | --------------------------------- |
| Shell config (zsh/tmux/p10k)                       | Claude Code plugins/agents/skills |
| Modern CLI tools (bat, eza, fd, rg, etc.)          | Website alias, SSH host colors    |
| Git config + global gitignore/gitattributes        | Mouseless config                  |
| Editor settings (VSCode/Cursor merge logic)        | Ghostty theme aliases             |
| Cleanup automation (Downloads/Screenshots)         | Specific API keys and gist IDs    |
| Gist sync (bidirectional SSH config/identity sync) | Cloud setup scripts (RunPod user) |
| BWS encrypted secrets workflow                     | Plugin marketplace selections     |

All personal values are centralized in [`config.sh`](./config.sh) — edit `DOTFILES_USERNAME`, `DOTFILES_REPO`, `GIST_SYNC_ID`, `GIT_USER_NAME`, and `GIT_USER_EMAIL` to make it yours.

## Rust CLI Tools

These modern alternatives are installed by default and significantly faster than their traditional counterparts:

| Tool                                                        | Replaces      | Why it's better                                          |
| ----------------------------------------------------------- | ------------- | -------------------------------------------------------- |
| [`bat`](https://github.com/sharkdp/bat)                     | `cat`         | Syntax highlighting, line numbers, git integration       |
| [`eza`](https://github.com/eza-community/eza)               | `ls`          | Colors, icons, git status, tree view built-in            |
| [`fd`](https://github.com/sharkdp/fd)                       | `find`        | Intuitive syntax, respects `.gitignore`, 5x faster       |
| [`ripgrep`](https://github.com/BurntSushi/ripgrep) (`rg`)   | `grep`        | Recursive by default, respects `.gitignore`, 10x+ faster |
| [`delta`](https://github.com/dandavison/delta)              | `diff`        | Side-by-side, syntax highlighting, line numbers          |
| [`zoxide`](https://github.com/ajeetdsouza/zoxide)           | `cd`          | Learns your habits, jump with `z dirname`                |
| [`dust`](https://github.com/bootandy/dust)                  | `du`          | Intuitive visualization of disk usage                    |
| [`jless`](https://github.com/PaulJuliusMartinez/jless)      | `less` (JSON) | Interactive JSON viewer with vim keybindings             |

**Extras** (`--extras` flag):

- [`hyperfine`](https://github.com/sharkdp/hyperfine) — statistical benchmarking with warmup and multiple runs
- [`gitui`](https://github.com/extrawurst/gitui) — TUI for git
- [`code2prompt`](https://github.com/mufeedvh/code2prompt) — generate LLM prompts from codebases

## Installation

### Step 1: Install dependencies

Install dependencies (e.g. oh-my-zsh and related plugins). The installer auto-detects your OS and applies sensible defaults.

```bash
# Install with defaults (recommended)
./install.sh

# Install only specific components
./install.sh --minimal --tmux --zsh  # --minimal disables all defaults
```

**Defaults by platform:**

| Platform  | Defaults                                                                            |
| --------- | ----------------------------------------------------------------------------------- |
| **macOS** | zsh, tmux, AI tools, cleanup + Rust CLI tools via Homebrew                          |
| **Linux** | zsh, tmux, AI tools, create-user + Rust CLI tools via [mise](https://mise.jdx.dev/) |

Installation on macOS requires Homebrew - install from [brew.sh](https://brew.sh/) first if needed.

### Step 2: Deploy configurations

Deploy configurations (sources aliases for .zshrc, applies oh-my-zsh settings, etc.). All settings live in [`config.sh`](./config.sh) — edit once, deploy everywhere.

```bash
# Deploy with defaults (recommended)
./deploy.sh

# Profiles
./deploy.sh --profile=server    # Safe base for shared machines
./deploy.sh --profile=minimal   # Nothing enabled — specify what you want

# Deploy only specific components
./deploy.sh --only vim claude   # Only vim and claude, nothing else

# Add to defaults
./deploy.sh --mouseless         # Defaults + mouseless
```

**Default components:**

- **Shell**: ZSH, tmux, vim, Powerlevel10k
- **Editors**: VSCode/Cursor/Antigravity (merged settings), Zed (symlinked config + keymap), `.editorconfig`, `.curlrc`, `.inputrc`
- **AI tools**: Claude Code, Codex CLI, Serena MCP, Ghostty terminal
- **Git**: gitconfig, global gitignore/gitattributes, global git hooks (secret detection)
- **Dev tools**: htop, pdb++, matplotlib styles, `claude-tools` Rust binary
- **Secrets**: GitHub gist sync, Bitwarden Secrets Manager (BWS)
- **Supply chain**: 7-day quarantine for npm/bun/pnpm/uv, weekly dep-audit
- **Automation**: file cleanup (macOS), Claude Code session cleanup, AI tools auto-update, package auto-update, text replacements sync (macOS)

**Flags are additive** — e.g., `./deploy.sh --mouseless` deploys defaults + mouseless. Use `--minimal` to disable all defaults, then specify only what you want.

## AI Assistants

### Claude Code (Primary AI Assistant)

This setup includes extensive [Claude Code](https://docs.anthropic.com/en/docs/claude-code) customization optimized for AI safety research:

```bash
./deploy.sh --claude  # Symlinks claude/ → ~/.claude
```

**What's included:**

- **`CLAUDE.md`** — Slim identity file (~55 lines) pointing at modular rules and docs
- **`rules/`** — 19 auto-loaded behavioral rules (safety, git, agents, refusal alternatives, supply-chain, browser automation, etc.)
- **`docs/`** — On-demand knowledge loaded by skills (research methodology, async patterns, tmux, agent teams)
- **`agents/`** — Personal agents (kept lean — most specialized agents live in plugins like `ai-safety-plugins`)
- **`skills/`** — Project-level slash commands: `/commit`, `/merge-worktree`, `/jobs`, `/modal`, `/log-gap`, `/recall-feedback`, `/mv-repo`, etc.
- **`hooks/`** — 40+ PreToolUse/PostToolUse/SessionStart scripts: approval classifier, secret blocking, modern-tool nudges, post-rebase guards, network audit
- **`templates/`** — Context profiles (`contexts/profiles.yaml`), research spec template

**Smart merge preserves your data** - if `~/.claude` already exists, credentials, history, and cache are automatically restored after symlinking.

#### Claude Code Plugin Marketplaces

Claude Code supports community plugin marketplaces. These are registered in [`claude/templates/contexts/profiles.yaml`](claude/templates/contexts/profiles.yaml) and synced via `claude-tools context --sync`:

| Marketplace                                                                         | What's in it                                                     |
| ----------------------------------------------------------------------------------- | ---------------------------------------------------------------- |
| **[claude-plugins-official](https://github.com/anthropics/claude-plugins-official)** | Superpowers, hookify, plugin-dev, commit-commands, productivity, engineering |
| **[ai-safety-plugins](https://github.com/yulonglin/ai-safety-plugins)**             | Research, writing, code, workflow, viz — for AI safety work      |
| **[productivity-tools](https://github.com/yulonglin/productivity-tools)**           | Personal productivity utilities                                  |
| **[ui-ux-pro-max-skill](https://github.com/nextlevelbuilder/ui-ux-pro-max-skill)**  | Design styles, palettes, production-grade frontend               |
| **[alignment-hive](https://github.com/Crazytieguy/alignment-hive)**                 | Alignment research utilities                                     |
| **[dev-browser-marketplace](https://github.com/sawyerhood/dev-browser)**            | Browser automation for development                               |
| **[openai-codex](https://github.com/crazytieguy/codex-plugin-cc)**                  | Codex CLI integration plugins                                    |

Profiles are managed via the `claude-tools context` CLI — compose multiple profiles to control which plugins load per-project:

```bash
claude-tools context code               # Software projects
claude-tools context code typescript python    # Compose multiple profiles
claude-tools context --list             # Show active plugins and available profiles
```

### Codex CLI (OpenAI)

[Codex CLI](https://github.com/openai/codex) configuration that reuses Claude Code's skills:

```bash
./deploy.sh --codex  # Symlinks codex/ → ~/.codex
```

**What's included:**

- **`AGENTS.md`** — Global instructions (references CLAUDE.md as source of truth)
- **`config.toml`** — Model settings, status line config, and per-project trust levels
- **`rules/`** — Behavioral rule files synced from Claude Code's `rules/`
- **`skills/`** → symlink to `claude/skills/` so both CLIs share the same skill set

The configuration follows the same research discipline as Claude Code but adapted for Codex's execution model.

### Antigravity CLI (Google) + OpenCode

Gemini CLI was retired by Google on **2026-06-18**; [Antigravity CLI](https://antigravity.google/docs/cli-features) (`agy`) is its official successor. [OpenCode](https://opencode.ai) is installed alongside as a model-agnostic OSS option. Both are installed by the `ai-tools` component.

Antigravity CLI can sync with Claude Code skills:

```bash
./scripts/sync_claude_to_antigravity.sh  # Symlinks Claude skills into agy
```

**What it does:**

- Symlinks Claude Code skills to `~/.gemini/antigravity-cli/skills/`
- Project instructions come from `AGENTS.md` (Antigravity reads it natively)

**Note:** Antigravity CLI is closed-source and brand-new; its skills/permissions schema differs from Claude's. The skills sync is adapted but untested end-to-end — permission sync is not yet ported (see the script header).

## Terminal & Shell

### Ghostty (Terminal Emulator)

[Ghostty](https://ghostty.org/) is a fast, GPU-accelerated terminal written in Zig. Config is symlinked to the platform-specific location:

```bash
./deploy.sh --ghostty  # Part of defaults
```

**Key settings in `config/ghostty.conf`:**

- `Cmd+C` triggers shell-based copy (integrates with tmux)
- `Shift+Enter` for multiline input
- Sensible font and color defaults

Config location: macOS `~/Library/Application Support/com.mitchellh.ghostty/config`, Linux `~/.config/ghostty/config`

#### Theme Aliases

Launch new Ghostty windows with different color themes - useful for visually distinguishing contexts:

Default Ghostty config uses Catppuccin Mocha. The `g0`–`g9` aliases launch a new window with a different theme:

| Alias | Theme                        | Character                          |
| ----- | ---------------------------- | ---------------------------------- |
| `g0`  | TokyoNight                   | Deep blue bg — neon city           |
| `g1`  | Dracula                      | Purple-grey bg — vibrant classic   |
| `g2`  | Nord                         | Arctic blue-grey bg — calm         |
| `g3`  | Rose Pine                    | Deep purple bg — botanical         |
| `g4`  | Kanagawa Dragon              | Warm near-black bg — Japanese ink  |
| `g5`  | Gruvbox Dark                 | Neutral warm bg — retro            |
| `g6`  | Everforest Dark Hard         | Green-grey bg — forest             |
| `g7`  | Solarized Dark Higher Contrast | Dark teal bg — high contrast     |
| `g8`  | Melange Dark                 | Warm brown bg — earthy             |
| `g9`  | Material Ocean               | Near-black bg — minimal            |

```bash
g1                        # Launch Ghostty with Dracula theme
gtheme "Tomorrow Night"   # Launch with any theme by name
ghostty +list-themes      # See all available themes
```

Each alias opens a **single fresh window** (no tab restoration) with the specified theme.

#### SSH Color Switching

Terminal colors automatically change when SSH-ing to help identify which machine you're on. Colors revert when the session ends.

```bash
ssh myserver     # In Ghostty: colors change automatically
sshc myserver    # Explicit color-changing SSH (works in any terminal)
```

**Configure per-host colors** by editing `SSH_HOST_COLORS` in `config/ssh_themes.sh`:

```bash
# Format: "background:foreground:cursor" in hex
SSH_HOST_COLORS[prod*]="#3d0000:#ffffff:#ff6666"      # Red-tinted for production
SSH_HOST_COLORS[dev*]="#002200:#ffffff:#66ff66"       # Green-tinted for dev
SSH_HOST_COLORS[gpu*]="#1a0033:#ffffff:#cc66ff"       # Purple for GPU servers
SSH_HOST_COLORS[default]="#0d1926:#c5d4dd:#88c0d0"    # Blue-gray fallback
```

Patterns support wildcards (`prod*` matches `prod1`, `prod-web`, etc.). The `default` key applies to any host without a specific match.

### Powerlevel10k Prompt

[Powerlevel10k](https://github.com/romkatv/powerlevel10k) provides a fast, feature-rich ZSH prompt. This config includes custom segments for SSH-aware machine identification.

**Requirements**: Install a [Nerd Font](https://github.com/romkatv/powerlevel10k#meslo-nerd-font-patched-for-powerlevel10k) for icons.

**Reconfigure**: Run `p10k configure` (when prompted, overwrite `p10k.zsh` but don't apply to `.zshrc`).

| Segment         | Description                                              |
| --------------- | -------------------------------------------------------- |
| **Remote host** | Machine name + emoji (SSH sessions only)                 |
| **Directory**   | Current path with git root highlighting                  |
| **Git status**  | Branch, dirty indicator, stash count                     |
| **Right side**  | Exit code, command duration, Python venv, cloud contexts |

#### SSH-Aware Machine Identification

When SSH'd to a remote machine, the prompt shows a **consistent machine name** derived from your SSH config:

```
🌊 mats ~/code/project (main)                   # Instead of: user@ip-172-31-42-17
```

Each machine gets a **unique emoji** based on its name hash, so you can visually distinguish machines at a glance.

**How it works:**

1. Looks up your public IP against `~/.ssh/config` `HostName` entries
2. Uses the matching `Host` alias as the display name
3. Falls back to abbreviated hostname if no match
4. Hashes the name to assign a stable emoji from a curated palette

**Example SSH config:**

```
Host mats
    HostName 203.0.113.42
    User yulong

Host hetzner-gpu
    HostName 198.51.100.10
    User root
```

SSH to `203.0.113.42` → prompt shows `🌊 mats` instead of the IP or hostname.

**Customization:**

- `SERVER_NAME` env var overrides everything
- `MACHINE_EMOJI` env var overrides the auto-assigned emoji

### Claude Code Statusline

Claude Code displays a custom statusline with session info. Configuration: `claude/settings.json` (`statusLine.command = "claude-tools statusline"`).

```
🌊 mats [code python] ~/code/project (main*) · 📊 45% · $0.23 · 12m
│        │             │              │      │        │        └─ Session duration
│        │             │              │      │        └─ Session cost
│        │             │              │      └─ Context usage (color-coded)
│        │             │              └─ Branch (* = dirty)
│        │             └─ Active Claude context profiles
│        └─ Directory
└─ Machine name (SSH only, same as p10k)
```

**Features:**

- **Machine name**: Uses same `machine-name` script as Powerlevel10k for consistency
- **Git info**: Branch with dirty indicator
- **Context %**: Color-coded usage (green <70%, yellow 70-89%, red 90%+)
- **Cost**: Running session total in USD
- **Duration**: Session runtime in minutes/hours

`ccusage statusline` is not wired into the live Claude hook path because it can OOM on large local histories; guard logic still uses lightweight `ccusage blocks --active --json` where available.

Both the shell prompt and Claude Code statusline use your SSH config aliases, so machine identification is consistent across tools.

### Ignore Pattern Management

`claude-tools ignore` manages per-repo `.gitignore` and `.ignore` patterns interactively.

```bash
claude-tools ignore                    # Launch TUI (same as `ignore apply`)
claude-tools ignore apply              # Interactive pattern selection
claude-tools ignore apply --dry-run    # Preview without writing
claude-tools ignore apply --non-interactive  # Apply defaults without TUI
claude-tools ignore status             # Show current managed patterns
```

The TUI shows patterns grouped by category with tri-state toggles:
- `[   ]` skip — pattern not applied
- `[ G ]` gitignore — added to `.gitignore` only
- `[G+S]` gitignore + searchable — added to `.gitignore` AND negated in `.ignore`

Patterns in `[G+S]` state are git-ignored but remain searchable by rg, fd, Claude Code, and Cursor. Pattern definitions live in `config/ignore/patterns`.

### Codex Statusline

Codex uses built-in status items configured in `codex/config.toml` under `[tui].status_line` (for example: model, current dir, git branch, weekly/5h limits, context remaining).

### SSH Key Management

Automatically adds your SSH key to ssh-agent on shell startup:

```bash
# Automatically enabled when you deploy ZSH config
./deploy.sh  # (default: includes ZSH)
```

**How it works:**

- Checks for `~/.ssh/id_ed25519` (customizable via `SSH_KEY_PATH` env var)
- **Prompts to generate** if key doesn't exist (never overwrites existing keys)
- Adds to macOS Keychain (`--apple-use-keychain`) or Linux ssh-agent
- Only runs in interactive shells
- Skips if key already loaded in agent

**First-time setup flow:**

1. Shell starts → detects no key → prompts "Generate a new ed25519 SSH key now? [y/N]"
2. If yes → generates key → shows command to copy public key
3. Automatically adds to agent on this and future shell sessions

**Custom key path:**

```bash
export SSH_KEY_PATH=~/.ssh/id_rsa  # Use RSA key instead
```

Configuration: [`config/ssh_setup.sh`](config/ssh_setup.sh)

## Dev Tools

### htop (Process Monitor)

Dynamic [htop](https://htop.dev/) configuration that adapts CPU meters to your core count:

```bash
./deploy.sh --htop  # Part of defaults
```

The config in `config/htop/htoprc` uses a dynamic layout that works across machines with different CPU counts—no manual adjustment needed.

### pdb++ (Python Debugger)

High-contrast color scheme for [pdb++](https://github.com/pdbpp/pdbpp), the enhanced Python debugger:

```bash
./deploy.sh --pdb  # Part of defaults
```

**Global config works with per-project installations**. The config is deployed to `~/.pdbrc.py` (symlinked), but pdb++is installed per-project via `uv add --dev pdbpp`. This works because pdb++ reads the global config at runtime.

**Auto-detects terminal background** using OSC 11 escape sequence:

- **Light terminals**: Dark colors on light background (solarized-light theme)
- **Dark terminals**: Bright colors on dark background (monokai theme)
- **Fallback**: Defaults to dark theme if detection fails (SSH, older terminals)

Detection succeeds in modern terminals (iTerm2, Ghostty, Kitty, Alacritty) and fails gracefully elsewhere.

**Test it works:**

```bash
cd /path/to/project
uv add --dev pdbpp
python -c "import pdb; pdb.set_trace()" <<< "c"
# Should show high-contrast colors
```

**Per-project override** (advanced): Create `.pdbrc.py` in project root. It takes precedence over the global config. See [pdb++ docs](https://github.com/pdbpp/pdbpp#configuration) for details.

## Automation

### Automatic Cleanup (macOS)

Scheduled cleanup of old files from `~/Downloads` and `~/Screenshots`:

```bash
./deploy.sh --cleanup  # Part of macOS defaults
```

**How it works:**

- Moves files older than 180 days (configurable) to **Trash** (not permanent delete)
- Runs monthly via launchd
- Only deletes files not accessed AND not modified in retention period

```bash
# Preview what would be cleaned
./scripts/cleanup/cleanup_old_files.sh --dry-run

# Custom retention (90 days) and schedule (weekly)
./scripts/cleanup/install.sh --days 90 --schedule weekly
```

See [`scripts/cleanup/README.md`](./scripts/cleanup/README.md) for full documentation.

### Claude Code Session Cleanup (both platforms)

Automatically kills idle Claude Code processes daily at 17:00:

```bash
./deploy.sh --claude-cleanup  # Part of defaults (both macOS and Linux)
```

**How it works:**

- Only kills processes with **no output activity for 24h** (preserves active + tmux sessions)
- Runs daily via launchd (macOS) or cron (Linux)
- Manual control via `clear-claude-code` command (aliases: `ccl`, `cci`, `ccf`)

```bash
# Check status
clear-claude-code --list

# Uninstall
./scripts/cleanup/setup_claude_cleanup.sh --uninstall
```

### AI Tools Auto-Update (both platforms)

Daily automatic updates for Claude Code, Codex CLI, OpenCode, and Antigravity CLI at 06:00:

```bash
./deploy.sh --ai-update  # Part of defaults
```

Runs via launchd (macOS) or cron (Linux). Uninstall with `scripts/cleanup/setup_ai_update.sh --uninstall`.

### Package Auto-Update (both platforms)

Weekly package upgrade + cleanup on Sundays at 05:00:

```bash
./deploy.sh --brew-update  # Part of defaults
```

Supports Homebrew (macOS), apt, dnf, and pacman (Linux). Includes cleanup of stale caches.

### Text Replacements (macOS)

Bidirectional sync between macOS text replacements and [Alfred](https://www.alfredapp.com/) snippets. Runs daily at 09:00:

```bash
./deploy.sh --text-replacements  # macOS only, part of defaults
```

macOS uses raw shortcuts; Alfred applies a collection prefix at runtime (e.g., `fm.hi`). Requires Full Disk Access for your terminal app.

## Secrets & Security

### Encrypted Secrets (Bitwarden Secrets Manager)

API keys are stored in [Bitwarden Secrets Manager](https://bitwarden.com/products/secrets-manager/) (BWS) — a hosted, team-shareable secrets vault. The CLI (`bws`) fetches secrets on demand; nothing is written to disk except a machine access token.

**File locations:**

| File | Location | Purpose |
|------|----------|---------|
| BWS token | `~/.config/bws/token` | Machine access token (paste from Bitwarden on new machines) |

**Commands:**

```bash
secrets-init bws         # First-time setup: save BWS access token
secrets-edit             # Add/update/delete secrets (fzf TUI or: secrets-edit KEY VALUE)
secrets-paths            # Show resolved backend + token path
```

**New machine setup:**

1. Run `./install.sh` (installs bws CLI)
2. Run `secrets-init bws` and paste your BWS access token from Bitwarden

**Per-project usage:** Run `setup-envrc` in any repo to create a `.envrc` that selectively exposes only the secrets that repo should see. It supports direct exports (`KEY`), renamed exports (`ENV_VAR=SECRET_NAME`), and a repo-specific Telegram plugin binding (`--telegram-secret SECRET_NAME`). If local `.env` files already exist, the TUI scans the repo root recursively and can offer to delete selected files.

`setup-envrc` tries `direnv allow` automatically. If that cannot update direnv's allowlist (for example in a sandboxed environment), it prints the manual `direnv allow .` command and still completes the rest of the setup.

### Gist Sync Automation (both platforms)

Automatically sync config with GitHub gist daily at 08:00:

```bash
./deploy.sh --secrets  # Part of defaults
```

**How it works:**

- Bidirectional sync with GitHub gist (SSH config, authorized_keys, git identity)
- Auto-adds local public key to `authorized_keys` (enables SSH between your machines)
- Last-modified wins: compares local vs gist timestamps
- Requires `gh auth login` (run once for authentication)
- Runs daily via launchd (macOS) or cron (Linux)

```bash
# Manual sync
sync-gist

# Uninstall automation
./scripts/cleanup/setup_gist_sync.sh --uninstall
```

> **Note:** Secret gists are unlisted, not encrypted. Only non-secret config (SSH config, authorized_keys, git identity) should be synced via gist.

### Global Git Hooks

Pre-commit hooks for secret detection across all repositories:

```bash
./deploy.sh --git-hooks  # Part of defaults
```

Scans staged files for API keys, tokens, and credentials before each commit.

### Supply Chain Defense

Multi-layer defense against npm/PyPI supply chain attacks (axios 2026, litellm 2026, shai-hulud 2025). Deployed automatically with `./deploy.sh`.

**What it does:**

| Layer | Defense | What it blocks |
|-------|---------|----------------|
| 7-day quarantine | `min-release-age` on all package managers | Freshly-published malicious versions (caught within days) |
| Script blocking | `ignore-scripts=true` in npm/pnpm | Postinstall scripts that exfiltrate secrets or install RATs |
| Credential isolation | API keys scoped per-project via direnv | Compromised package in project A can't read project B's keys |
| Lockfile scanning | Pre-commit hook checks changed lockfiles | Known-bad packages entering your lockfile |
| Weekly audit | Scans all repos for known-bad IOCs | Packages you already have that were later found compromised |
| Claude Code hook | Warns before any `npm install` / `pip install` | AI assistant installing packages without checking them first |

**Day-to-day workflow:**

```bash
# Installing packages works normally — quarantine is transparent
npm install express          # Works (express is >7 days old)
bun add zod                  # Works
uv add httpx                 # Works

# New packages published <7 days ago are blocked (intentional)
npm install some-brand-new-pkg
# Error: min-release-age — package was published 2 days ago

# Override for a specific install (after checking it's safe)
npm install --min-release-age=0 some-brand-new-pkg   # npm
bun add --minimumReleaseAge=0 some-brand-new-pkg      # bun
UV_EXCLUDE_NEWER= uv pip install some-brand-new-pkg   # uv
```

**Credential isolation:**

API keys stay in `$DOTFILES_SECRETS_DIR/secrets.env.enc` and are NOT globally exported. Each project gets only the keys it needs:

```bash
# Interactive picker (fzf)
cd ~/code/my-project
setup-envrc                  # Select keys with TAB, confirm with ENTER
# → Creates .envrc with eval-based exports, direnv auto-loads on cd

# Non-interactive
setup-envrc ANTHROPIC_API_KEY OPENAI_API_KEY

# Map a namespaced secret into the env var your app expects
setup-envrc ANTHROPIC_API_KEY TELEGRAM_BOT_TOKEN=NUDGE_TELEGRAM_BOT_TOKEN

# Claude Telegram plugin: keep the token canonical in dotfiles-secrets,
# and generate .claude/channels/telegram/.env only at launch time
setup-envrc --telegram-secret AMBASSADOR_TELEGRAM_BOT_TOKEN

# Check what's configured
setup-envrc --list           # Show keys in current .envrc
setup-envrc --clean          # Remove .envrc

# One-off command with selected keys (no .envrc needed)
with-secrets ANTHROPIC_API_KEY OPENAI_API_KEY -- python my_script.py
```

**Manual audit:**

```bash
dep-audit                    # Scan all repos for known-bad packages now
# Runs automatically every Sunday at 10 AM
```

**Config files deployed:**

| File | Deployed to | Purpose |
|------|-------------|---------|
| `config/npmrc` | `~/.npmrc` | `ignore-scripts=true` + `min-release-age=7` |
| `config/bunfig.toml` | `~/.bunfig.toml` | `minimumReleaseAge=604800` (seconds) |
| `config/pnpmrc` | `~/Library/Preferences/pnpm/rc` | `minimum-release-age=10080` (minutes) |
| `config/uv.toml` | `~/.config/uv/uv.toml` | `exclude-newer` (via `UV_EXCLUDE_NEWER` env var) |

**Selective deploy:**

```bash
./deploy.sh --only pkg-configs    # Just package manager configs
./deploy.sh --no-pkg-configs      # Everything except package configs
./deploy.sh --only dep-audit      # Just the weekly audit
```

## Getting to know these dotfiles

- Any software or command line tools you need, add them to the [install.sh](./install.sh) script. Try adding a new command line tool to the install script.
- Any new plugins or environment setup, add them to the [config/zshrc.sh](./config/zshrc.sh) script.
- Any aliases you need, add them to the relevant `config/aliases/<theme>.sh` file (git.sh for git, nav.sh for navigation, net.sh for network/system, etc.). Try adding your own alias to the bottom of the matching file. For example, try setting `cd1` to your most used git repo so you can just type `cd1` to get to it.
- **Utility functions** in `config/modern_tools.sh`: `mkd` (mkdir+cd), `cdf` (cd to Finder window, macOS), `targz` (smart compression), `dataurl`, `digga` (DNS lookup), `getcertnames` (SSL certs), `o` (cross-platform open), `server` (quick HTTP server)
- **System aliases** in `config/aliases/net.sh`: `flush` (DNS cache), `afk` (lock screen, macOS), `week` (ISO week number)

## Cloud Setup (RunPod, Hetzner, etc.)

One-command setup for cloud VMs and containers:

```bash
# RunPod (fresh pod, as root)
curl -fsSL https://raw.githubusercontent.com/yulonglin/dotfiles/main/scripts/cloud/setup.sh | bash

# After pod restart (recreates user entry)
curl -fsSL https://raw.githubusercontent.com/yulonglin/dotfiles/main/scripts/cloud/restart.sh | bash

# Hetzner / standard VPS (persistent /home)
curl -fsSL https://raw.githubusercontent.com/yulonglin/dotfiles/main/scripts/cloud/setup.sh | USER_HOME=/home bash
```

Then SSH as `yulong@<ip>` (not root). Runs the lean `cloud` profile and provisions the `main` branch by default — pin another with `| bash -s -- --branch <name>` or `DOTFILES_BRANCH=<name>`. See [`scripts/cloud/README.md`](./scripts/cloud/README.md) for details.

**What it does:**

- Creates non-root user in persistent storage (`/workspace/yulong` on RunPod)
- Installs uv, dotfiles, Claude Code
- Copies SSH keys for direct access

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