@bastani/atomic 0.8.10 → 0.8.12-0

package/docs/sessions.md

@@ -1,17 +1,17 @@
 # Sessions
 
-Pi saves conversations as sessions so you can continue work, branch from earlier turns, and revisit previous paths.
+Atomic saves conversations as sessions so you can continue work, branch from earlier turns, and revisit previous paths.
 
 ## Session Storage
 
-Sessions auto-save to `~/.pi/agent/sessions/`, organized by working directory. Each session is a JSONL file with a tree structure.
+Sessions auto-save to `~/.atomic/agent/sessions/`, organized by working directory. Each session is a JSONL file with a tree structure.
 
 ```bash
-pi -c                  # Continue most recent session
-pi -r                  # Browse and select from past sessions
-pi --no-session        # Ephemeral mode; do not save
-pi --session <path|id> # Use a specific session file or partial session ID
-pi --fork <path|id>    # Fork a session file or partial session ID into a new session
+atomic -c                  # Continue most recent session
+atomic -r                  # Browse and select from past sessions
+atomic --no-session        # Ephemeral mode; do not save
+atomic --session <path|id> # Use a specific session file or partial session ID
+atomic --fork <path|id>    # Fork a session file or partial session ID into a new session
 ```
 
 Use `/session` in interactive mode to see the current session file, session ID, message count, tokens, and cost.
@@ -35,7 +35,7 @@ For the JSONL file format and SessionManager API, see [Session Format](session-f
 
 ## Resuming and Deleting Sessions
 
-`/resume` opens an interactive session picker for the current project. `pi -r` opens the same picker at startup.
+`/resume` opens an interactive session picker for the current project. `atomic -r` opens the same picker at startup.
 
 In the picker you can:
 
@@ -46,7 +46,7 @@ In the picker you can:
 - rename with CTRL+R
 - delete with CTRL+D, then confirm
 
-When available, pi uses the `trash` CLI for deletion instead of permanently removing files.
+When available, Atomic uses the `trash` CLI for deletion instead of permanently removing files.
 
 ## Naming Sessions
 
@@ -56,7 +56,7 @@ Use `/name <name>` to set a human-readable session name:
 /name Refactor auth module
 ```
 
-Named sessions are easier to find in `/resume` and `pi -r`.
+Named sessions are easier to find in `/resume` and `atomic -r`.
 
 ## Branching with `/tree`
 
@@ -120,7 +120,7 @@ Use `/tree` when you want to keep alternatives together. Use `/fork` or `/clone`
 
 ## Branch Summaries
 
-When `/tree` switches away from one branch to another, pi can summarize the abandoned branch and attach that summary at the new position. This preserves important context from the path you left without replaying the whole branch.
+When `/tree` switches away from one branch to another, Atomic can summarize the abandoned branch and attach that summary at the new position. This preserves important context from the path you left without replaying the whole branch.
 
 When prompted, choose one of:
 

package/docs/settings.md

@@ -1,13 +1,13 @@
 # Settings
 
-Pi uses JSON settings files with project settings overriding global settings.
+Atomic uses JSON settings files with project settings overriding global settings.
 
 | Location | Scope |
 |----------|-------|
-| `~/.pi/agent/settings.json` | Global (all projects) |
-| `.pi/settings.json` | Project (current directory) |
+| `~/.atomic/agent/settings.json` | Global (all projects) |
+| `.atomic/settings.json` | Project (current directory) |
 
-Edit directly or use `/settings` for common options.
+Edit directly or use `/settings` for common options. Atomic reads legacy `~/.pi/agent/settings.json` and `.pi/settings.json` as compatibility fallbacks, with `.atomic` paths taking precedence.
 
 ## All Settings
 
@@ -50,9 +50,9 @@ Edit directly or use `/settings` for common options.
 
 ### Telemetry and update checks
 
-`enableInstallTelemetry` only controls the anonymous install/update ping to `https://pi.dev/api/report-install`. Opting out of telemetry does not disable update checks; Pi can still fetch `https://pi.dev/api/latest-version` to look for the latest version.
+`enableInstallTelemetry` only controls the anonymous install/update ping to `https://pi.dev/api/report-install`. Opting out of telemetry does not disable update checks; Atomic can still fetch the npm registry latest package metadata at `https://registry.npmjs.org/@bastani/atomic/latest` to look for the latest version.
 
-Set `PI_SKIP_VERSION_CHECK=1` to disable the Pi version update check. Use `--offline` or `PI_OFFLINE=1` to disable all startup network operations described here, including update checks, package update checks, and install/update telemetry.
+Set `ATOMIC_SKIP_VERSION_CHECK=1` to disable the Atomic version update check. Use `--offline` or `ATOMIC_OFFLINE=1` to disable all startup network operations described here, including update checks, package update checks, and install/update telemetry. Legacy `PI_*` aliases are also supported for app-specific environment variables.
 
 ### Warnings
 
@@ -164,10 +164,10 @@ Normally the package manager's global modules location is queried using `root -g
 | `sessionDir` | string | - | Directory where session files are stored. Accepts absolute or relative paths, plus `~`. |
 
 ```json
-{ "sessionDir": ".pi/sessions" }
+{ "sessionDir": ".atomic/sessions" }
 ```
 
-When multiple sources specify a session directory, precedence is `--session-dir`, `PI_CODING_AGENT_SESSION_DIR`, then `sessionDir` in settings.json.
+When multiple sources specify a session directory, precedence is `--session-dir`, `ATOMIC_CODING_AGENT_SESSION_DIR`, then `sessionDir` in settings.json.
 
 ### Model Cycling
 
@@ -189,9 +189,9 @@ When multiple sources specify a session directory, precedence is `--session-dir`
 
 ### Resources
 
-These settings define where to load extensions, skills, prompts, and themes from.
+These settings define where to load extensions, skills, prompts, themes, and workflows from.
 
-Paths in `~/.pi/agent/settings.json` resolve relative to `~/.pi/agent`. Paths in `.pi/settings.json` resolve relative to `.pi`. Absolute paths and `~` are supported.
+Paths in `~/.atomic/agent/settings.json` resolve relative to `~/.atomic/agent`. Paths in `.atomic/settings.json` resolve relative to `.atomic`. Absolute paths and `~` are supported.
 
 | Setting | Type | Default | Description |
 |---------|------|---------|-------------|
@@ -200,6 +200,7 @@ Paths in `~/.pi/agent/settings.json` resolve relative to `~/.pi/agent`. Paths in
 | `skills` | string[] | `[]` | Local skill file paths or directories |
 | `prompts` | string[] | `[]` | Local prompt template paths or directories |
 | `themes` | string[] | `[]` | Local theme file paths or directories |
+| `workflows` | string[] | `[]` | Local workflow file paths or directories |
 | `enableSkillCommands` | boolean | `true` | Register skills as `/skill:name` commands |
 
 Arrays support glob patterns and exclusions. Use `!pattern` to exclude. Use `+path` to force-include an exact path and `-path` to force-exclude an exact path.
@@ -222,7 +223,8 @@ Object form filters which resources to load:
     {
       "source": "pi-skills",
       "skills": ["brave-search", "transcribe"],
-      "extensions": []
+      "extensions": [],
+      "workflows": []
     }
   ]
 }
@@ -251,22 +253,23 @@ See [packages.md](packages.md) for package management details.
   "warnings": {
     "anthropicExtraUsage": true
   },
-  "packages": ["pi-skills"]
+  "packages": ["pi-skills"],
+  "workflows": ["./workflows/*.ts"]
 }
 ```
 
 ## Project Overrides
 
-Project settings (`.pi/settings.json`) override global settings. Nested objects are merged:
+Project settings (`.atomic/settings.json`) override global settings. Nested objects are merged:
 
 ```json
-// ~/.pi/agent/settings.json (global)
+// ~/.atomic/agent/settings.json (global)
 {
   "theme": "dark",
   "compaction": { "enabled": true, "reserveTokens": 16384 }
 }
 
-// .pi/settings.json (project)
+// .atomic/settings.json (project)
 {
   "compaction": { "reserveTokens": 8192 }
 }

package/docs/shell-aliases.md

@@ -1,8 +1,8 @@
 # Shell Aliases
 
-Pi runs bash in non-interactive mode (`bash -c`), which doesn't expand aliases by default.
+Atomic runs bash in non-interactive mode (`bash -c`), which doesn't expand aliases by default.
 
-To enable your shell aliases, add to `~/.pi/agent/settings.json`:
+To enable your shell aliases, add to `~/.atomic/agent/settings.json` (legacy `~/.pi/agent/settings.json` is also read):
 
 ```json
 {

package/docs/skills.md

@@ -1,10 +1,10 @@
-> pi can create skills. Ask it to build one for your use case.
+> Atomic can create skills. Ask it to build one for your use case.
 
 # Skills
 
 Skills are self-contained capability packages that the agent loads on-demand. A skill provides specialized workflows, setup instructions, helper scripts, and reference documentation for specific tasks.
 
-Pi implements the [Agent Skills standard](https://agentskills.io/specification), warning about violations but remaining lenient.
+Atomic implements the [Agent Skills standard](https://agentskills.io/specification), warning about violations but remaining lenient.
 
 ## Table of Contents
 
@@ -21,20 +21,20 @@ Pi implements the [Agent Skills standard](https://agentskills.io/specification),
 
 > **Security:** Skills can instruct the model to perform any action and may include executable code the model invokes. Review skill content before use.
 
-Pi loads skills from:
+Atomic loads skills from:
 
 - Global:
-  - `~/.pi/agent/skills/`
+  - `~/.atomic/agent/skills/` (legacy `~/.pi/agent/skills/`)
   - `~/.agents/skills/`
 - Project:
-  - `.pi/skills/`
+  - `.atomic/skills/` (legacy `.pi/skills/`)
   - `.agents/skills/` in `cwd` and ancestor directories (up to git repo root, or filesystem root when not in a repo)
-- Packages: `skills/` directories or `pi.skills` entries in `package.json`
+- Packages: `skills/` directories, `atomic.skills`, or legacy `pi.skills` entries in `package.json`
 - Settings: `skills` array with files or directories
 - CLI: `--skill <path>` (repeatable, additive even with `--no-skills`)
 
 Discovery rules:
-- In `~/.pi/agent/skills/` and `.pi/skills/`, direct root `.md` files are discovered as individual skills
+- In `~/.atomic/agent/skills/` and `.atomic/skills/` (plus legacy `~/.pi/agent/skills/` and `.pi/skills/`), direct root `.md` files are discovered as individual skills
 - In all skill locations, directories containing `SKILL.md` are discovered recursively
 - In `~/.agents/skills/` and project `.agents/skills/`, root `.md` files are ignored
 
@@ -53,7 +53,7 @@ To use skills from Claude Code or OpenAI Codex, add their directories to setting
 }
 ```
 
-For project-level Claude Code skills, add to `.pi/settings.json`:
+For project-level Claude Code skills, add to `.atomic/settings.json` (legacy `.pi/settings.json` is also supported):
 
 ```json
 {
@@ -63,7 +63,7 @@ For project-level Claude Code skills, add to `.pi/settings.json`:
 
 ## How Skills Work
 
-1. At startup, pi scans skill locations and extracts names and descriptions
+1. At startup, Atomic scans skill locations and extracts names and descriptions
 2. The system prompt includes available skills in XML format per the [specification](https://agentskills.io/integrate-skills)
 3. When a task matches, the agent uses `read` to load the full SKILL.md (models don't always do this; use prompting or `/skill:name` to force it)
 4. The agent follows the instructions, using relative paths to reference scripts and assets
@@ -175,7 +175,7 @@ description: Helps with PDFs.
 
 ## Validation
 
-Pi validates skills against the Agent Skills standard. Most issues produce warnings but still load the skill:
+Atomic validates skills against the Agent Skills standard. Most issues produce warnings but still load the skill:
 
 - Name doesn't match parent directory
 - Name exceeds 64 characters or contains invalid characters
@@ -229,4 +229,4 @@ cd /path/to/brave-search && npm install
 ## Skill Repositories
 
 - [Anthropic Skills](https://github.com/anthropics/skills) - Document processing (docx, pdf, pptx, xlsx), web development
-- [Pi Skills](https://github.com/badlogic/pi-skills) - Web search, browser automation, Google APIs, transcription
+- [Pi Skills](https://github.com/badlogic/pi-skills) - Upstream skill examples for web search, browser automation, Google APIs, and transcription

package/docs/terminal-setup.md

@@ -1,6 +1,6 @@
 # Terminal Setup
 
-Pi uses the [Kitty keyboard protocol](https://sw.kovidgoyal.net/kitty/keyboard-protocol/) for reliable modifier key detection. Most modern terminals support this protocol, but some require configuration.
+Atomic uses the [Kitty keyboard protocol](https://sw.kovidgoyal.net/kitty/keyboard-protocol/) for reliable modifier key detection. Most modern terminals support this protocol, but some require configuration.
 
 ## Kitty, iTerm2
 
@@ -20,15 +20,15 @@ Older Claude Code versions may have added this Ghostty mapping:
 keybind = shift+enter=text:\n
 ```
 
-That mapping sends a raw linefeed byte. Inside pi, that is indistinguishable from `CTRL+J`, so tmux and pi no longer see a real `shift+enter` key event.
+That mapping sends a raw linefeed byte. Inside Atomic, that is indistinguishable from `CTRL+J`, so tmux and Atomic no longer see a real `shift+enter` key event.
 
 If Claude Code 2.x or newer is the only reason you added that mapping, you can remove it, unless you want to use Claude Code in tmux, where it still requires that Ghostty mapping.
 
-If you want `SHIFT+Enter` to keep working in tmux via that remap, add `ctrl+j` to your pi `newLine` keybinding in `~/.pi/agent/keybindings.json`:
+If you want `SHIFT+Enter` to keep working in tmux via that remap, add `ctrl+j` to your Atomic `tui.input.newLine` keybinding in `~/.atomic/agent/keybindings.json`:
 
 ```json
 {
-  "newLine": ["shift+enter", "ctrl+j"]
+  "tui.input.newLine": ["shift+enter", "ctrl+j"]
 }
 ```
 
@@ -63,7 +63,7 @@ Add to `keybindings.json` to enable `SHIFT+Enter` for multi-line input:
 
 ## Windows Terminal
 
-Add to `settings.json` (CTRL+SHIFT+, or Settings → Open JSON file) to forward the modified Enter keys pi uses:
+Add to `settings.json` (CTRL+SHIFT+, or Settings → Open JSON file) to forward the modified Enter keys Atomic uses:
 
 ```json
 {
@@ -81,8 +81,8 @@ Add to `settings.json` (CTRL+SHIFT+, or Settings → Open JSON file) to forward
 ```
 
 - `SHIFT+Enter` inserts a new line.
-- Windows Terminal binds `ALT+Enter` to fullscreen by default. That prevents pi from receiving `ALT+Enter` for follow-up queueing.
-- Remapping `ALT+Enter` to `sendInput` forwards the real key chord to pi instead.
+- Windows Terminal binds `ALT+Enter` to fullscreen by default. That prevents Atomic from receiving `ALT+Enter` for follow-up queueing.
+- Remapping `ALT+Enter` to `sendInput` forwards the real key chord to Atomic instead.
 
 If you already have an `actions` array, add the objects to it. If the old fullscreen behavior persists, fully close and reopen Windows Terminal.
 
@@ -101,6 +101,6 @@ For the best experience, use a terminal that supports the Kitty keyboard protoco
 
 The built-in terminal has limited escape sequence support. SHIFT+Enter cannot be distinguished from Enter in IntelliJ's terminal.
 
-If you want the hardware cursor visible, set `PI_HARDWARE_CURSOR=1` before running pi (disabled by default for compatibility).
+If you want the hardware cursor visible, set `ATOMIC_HARDWARE_CURSOR=1` before running Atomic. The legacy `PI_HARDWARE_CURSOR=1` alias also works; the hardware cursor is disabled by default for compatibility.
 
 Consider using a dedicated terminal emulator for the best experience.

package/docs/termux.md

@@ -1,6 +1,6 @@
 # Termux (Android) Setup
 
-Pi runs on Android via [Termux](https://termux.dev/), a terminal emulator and Linux environment for Android.
+Atomic runs on Android via [Termux](https://termux.dev/), a terminal emulator and Linux environment for Android.
 
 ## Prerequisites
 
@@ -16,14 +16,14 @@ pkg update && pkg upgrade
 # Install dependencies
 pkg install nodejs termux-api git
 
-# Install pi
+# Install Atomic
 npm install -g @bastani/atomic
 
 # Create config directory
-mkdir -p ~/.pi/agent
+mkdir -p ~/.atomic/agent
 
-# Run pi
-pi
+# Run Atomic
+atomic
 ```
 
 ## Clipboard Support
@@ -34,7 +34,7 @@ Image clipboard is not supported on Termux (the `ctrl+v` image paste feature wil
 
 ## Example AGENTS.md for Termux
 
-Create `~/.pi/agent/AGENTS.md` to help the agent understand the Termux environment:
+Create `~/.atomic/agent/AGENTS.md` to help the agent understand the Termux environment:
 
 ````markdown
 # Agent Environment: Termux on Android

package/docs/themes.md

@@ -1,4 +1,4 @@
-> pi can create themes. Ask it to build one for your setup.
+> Atomic can create themes. Ask it to build one for your setup.
 
 # Themes
 
@@ -16,12 +16,12 @@ Themes are JSON files that define colors for the TUI.
 
 ## Locations
 
-Pi loads themes from:
+Atomic loads themes from:
 
 - Built-in: `dark`, `light`, `catppuccin-frappe`, `catppuccin-latte`, `catppuccin-macchiato`, `catppuccin-mocha`
-- Global: `~/.pi/agent/themes/*.json`
-- Project: `.pi/themes/*.json`
-- Packages: `themes/` directories or `pi.themes` entries in `package.json`
+- Global: `~/.atomic/agent/themes/*.json` (legacy `~/.pi/agent/themes/*.json`)
+- Project: `.atomic/themes/*.json` (legacy `.pi/themes/*.json`)
+- Packages: `themes/` directories, `atomic.themes`, or legacy `pi.themes` entries in `package.json`
 - Settings: `themes` array with files or directories
 - CLI: `--theme <path>` (repeatable)
 
@@ -37,15 +37,15 @@ Select a theme via `/settings` or in `settings.json`:
 }
 ```
 
-On first run, pi detects your terminal background and defaults to `dark` or `light`.
+On first run, Atomic detects your terminal background and defaults to `dark` or `light`.
 
 ## Creating a Custom Theme
 
 1. Create a theme file:
 
 ```bash
-mkdir -p ~/.pi/agent/themes
-vim ~/.pi/agent/themes/my-theme.json
+mkdir -p ~/.atomic/agent/themes
+vim ~/.atomic/agent/themes/my-theme.json
 ```
 
 2. Define the theme with all required colors (see [Color Tokens](#color-tokens)):
@@ -116,7 +116,7 @@ vim ~/.pi/agent/themes/my-theme.json
 
 3. Select the theme via `/settings`.
 
-**Hot reload:** When you edit the currently active custom theme file, pi reloads it automatically for immediate visual feedback.
+**Hot reload:** When you edit the currently active custom theme file, Atomic reloads it automatically for immediate visual feedback.
 
 ## Theme Format
 
@@ -268,7 +268,7 @@ Four formats are supported:
 
 ### Terminal Compatibility
 
-Pi uses 24-bit RGB colors. Most modern terminals support this (iTerm2, Kitty, WezTerm, Windows Terminal, VS Code). For older terminals with only 256-color support, pi falls back to the nearest approximation.
+Atomic uses 24-bit RGB colors. Most modern terminals support this (iTerm2, Kitty, WezTerm, Windows Terminal, VS Code). For older terminals with only 256-color support, Atomic falls back to the nearest approximation.
 
 Check truecolor support:
 

package/docs/tui.md

@@ -1,4 +1,4 @@
-> pi can create TUI components. Ask it to build one for your use case.
+> Atomic can create TUI components. Ask it to build one for your use case.
 
 # TUI Components
 
@@ -448,7 +448,8 @@ interface MyTheme {
 Set `PI_TUI_WRITE_LOG` to capture the raw ANSI stream written to stdout.
 
 ```bash
-PI_TUI_WRITE_LOG=/tmp/tui-ansi.log npx tsx packages/tui/test/chat-simple.ts
+# Upstream pi-tui debug env example
+PI_TUI_WRITE_LOG=/tmp/tui-ansi.log bunx tsx packages/tui/test/chat-simple.ts
 ```
 
 ## Performance
@@ -737,7 +738,7 @@ ctx.ui.setStatus("my-ext", undefined);
 
 ### Pattern 4b: Working Indicator Customization
 
-Customize the inline working indicator shown while pi is streaming a response.
+Customize the inline working indicator shown while Atomic is streaming a response.
 
 ```typescript
 // Static indicator
@@ -757,7 +758,7 @@ ctx.ui.setWorkingIndicator({
 // Hide the indicator entirely
 ctx.ui.setWorkingIndicator({ frames: [] });
 
-// Restore pi's default spinner
+// Restore Atomic's default spinner
 ctx.ui.setWorkingIndicator();
 ```
 

package/docs/usage.md

@@ -1,4 +1,4 @@
-# Using Pi
+# Using Atomic
 
 This page collects day-to-day usage details that do not fit on the quickstart page.
 
@@ -53,7 +53,7 @@ Type `/` in the editor to open command completion. Extensions can register custo
 | `/reload` | Reload keybindings, extensions, skills, prompts, and context files |
 | `/hotkeys` | Show all keyboard shortcuts |
 | `/changelog` | Display version history |
-| `/quit` | Quit pi |
+| `/quit` | Quit Atomic |
 
 ## Message Queue
 
@@ -64,20 +64,20 @@ You can submit messages while the agent is still working:
 - **Escape** aborts and restores queued messages to the editor.
 - **ALT+Up** retrieves queued messages back to the editor.
 
-On Windows Terminal, ALT+Enter is fullscreen by default. Remap it as described in [Terminal setup](terminal-setup.md) if you want pi to receive the shortcut.
+On Windows Terminal, ALT+Enter is fullscreen by default. Remap it as described in [Terminal setup](terminal-setup.md) if you want Atomic to receive the shortcut.
 
 Configure delivery in [Settings](settings.md) with `steeringMode` and `followUpMode`.
 
 ## Sessions
 
-Sessions are saved automatically to `~/.pi/agent/sessions/`, organized by working directory.
+Sessions are saved automatically to `~/.atomic/agent/sessions/`, organized by working directory.
 
 ```bash
-pi -c                  # Continue most recent session
-pi -r                  # Browse and select a session
-pi --no-session        # Ephemeral mode; do not save
-pi --session <path|id> # Use a specific session file or session ID
-pi --fork <path|id>    # Fork a session into a new session file
+atomic -c                  # Continue most recent session
+atomic -r                  # Browse and select a session
+atomic --no-session        # Ephemeral mode; do not save
+atomic --session <path|id> # Use a specific session file or session ID
+atomic --fork <path|id>    # Fork a session into a new session file
 ```
 
 Useful session commands:
@@ -92,9 +92,9 @@ See [Sessions](sessions.md) and [Compaction](compaction.md) for details.
 
 ## Context Files
 
-Pi loads `AGENTS.md` or `CLAUDE.md` at startup from:
+Atomic loads `AGENTS.md` or `CLAUDE.md` at startup from:
 
-- `~/.pi/agent/AGENTS.md` for global instructions
+- `~/.atomic/agent/AGENTS.md` for global instructions
 - parent directories, walking up from the current working directory
 - the current directory
 
@@ -104,8 +104,8 @@ Use context files for project conventions, commands, safety rules, and preferenc
 
 Replace the default system prompt with:
 
-- `.pi/SYSTEM.md` for a project
-- `~/.pi/agent/SYSTEM.md` globally
+- `.atomic/SYSTEM.md` for a project
+- `~/.atomic/agent/SYSTEM.md` globally
 
 Append to the default prompt without replacing it with `APPEND_SYSTEM.md` in either location.
 
@@ -115,29 +115,29 @@ Use `/export [file]` to write a session to HTML.
 
 Use `/share` to upload a private GitHub gist with a shareable HTML link.
 
-If you use pi for open source work and want to publish sessions for model, prompt, tool, and evaluation research, see [`badlogic/pi-share-hf`](https://github.com/badlogic/pi-share-hf). It publishes sessions to Hugging Face datasets.
+If you use Atomic for open source work and want to publish sessions for model, prompt, tool, and evaluation research, see [`badlogic/pi-share-hf`](https://github.com/badlogic/pi-share-hf). It publishes sessions to Hugging Face datasets.
 
 ## CLI Reference
 
 ```bash
-pi [options] [@files...] [messages...]
+atomic [options] [@files...] [messages...]
 ```
 
 ### Package Commands
 
 ```bash
-pi install <source> [-l]     # Install package, -l for project-local
-pi remove <source> [-l]      # Remove package
-pi uninstall <source> [-l]   # Alias for remove
-pi update [source|self|pi]   # Update pi and packages; skips pinned packages
-pi update --extensions       # Update packages only
-pi update --self             # Update pi only
-pi update --extension <src>  # Update one package
-pi list                      # List installed packages
-pi config                    # Enable/disable package resources
+atomic install <source> [-l]     # Install package, -l for project-local
+atomic remove <source> [-l]      # Remove package
+atomic uninstall <source> [-l]   # Alias for remove
+atomic update [source|self|atomic] # Update Atomic and packages; skips pinned packages
+atomic update --extensions       # Update packages only
+atomic update --self             # Update Atomic only
+atomic update --extension <src>  # Update one package
+atomic list                      # List installed packages
+atomic config                    # Enable/disable package resources
 ```
 
-See [Pi Packages](packages.md) for package sources and security notes.
+See [Atomic Packages](packages.md) for package sources and security notes.
 
 ### Modes
 
@@ -149,10 +149,10 @@ See [Pi Packages](packages.md) for package sources and security notes.
 | `--mode rpc` | RPC mode over stdin/stdout; see [RPC mode](rpc.md) |
 | `--export <in> [out]` | Export a session to HTML |
 
-In print mode, pi also reads piped stdin and merges it into the initial prompt:
+In print mode, Atomic also reads piped stdin and merges it into the initial prompt:
 
 ```bash
-cat README.md | pi -p "Summarize this text"
+cat README.md | atomic -p "Summarize this text"
 ```
 
 ### Model Options
@@ -185,7 +185,7 @@ cat README.md | pi -p "Summarize this text"
 | `--no-builtin-tools`, `-nbt` | Disable built-in tools but keep extension/custom tools enabled |
 | `--no-tools`, `-nt` | Disable all tools |
 
-Built-in tools: `read`, `bash`, `edit`, `write`, `grep`, `find`, `ls`.
+Default built-in tools: `read`, `bash`, `edit`, `write`, `ask_user_question`, `todo`. Additional built-in read-only tools are available through tool options: `grep`, `find`, `ls`.
 
 ### Resource Options
 
@@ -204,7 +204,7 @@ Built-in tools: `read`, `bash`, `edit`, `write`, `grep`, `find`, `ls`.
 Combine `--no-*` with explicit flags to load exactly what you need, ignoring settings. Example:
 
 ```bash
-pi --no-extensions -e ./my-extension.ts
+atomic --no-extensions -e ./my-extension.ts
 ```
 
 ### Other Options
@@ -222,56 +222,56 @@ pi --no-extensions -e ./my-extension.ts
 Prefix files with `@` to include them in the message:
 
 ```bash
-pi @prompt.md "Answer this"
-pi -p @screenshot.png "What's in this image?"
-pi @code.ts @test.ts "Review these files"
+atomic @prompt.md "Answer this"
+atomic -p @screenshot.png "What's in this image?"
+atomic @code.ts @test.ts "Review these files"
 ```
 
 ### Examples
 
 ```bash
 # Interactive with initial prompt
-pi "List all .ts files in src/"
+atomic "List all .ts files in src/"
 
 # Non-interactive
-pi -p "Summarize this codebase"
+atomic -p "Summarize this codebase"
 
 # Non-interactive with piped stdin
-cat README.md | pi -p "Summarize this text"
+cat README.md | atomic -p "Summarize this text"
 
 # Different model
-pi --provider openai --model gpt-4o "Help me refactor"
+atomic --provider openai --model gpt-4o "Help me refactor"
 
 # Model with provider prefix
-pi --model openai/gpt-4o "Help me refactor"
+atomic --model openai/gpt-4o "Help me refactor"
 
 # Model with thinking level shorthand
-pi --model sonnet:high "Solve this complex problem"
+atomic --model sonnet:high "Solve this complex problem"
 
 # Limit model cycling
-pi --models "claude-*,gpt-4o"
+atomic --models "claude-*,gpt-4o"
 
 # Read-only mode
-pi --tools read,grep,find,ls -p "Review the code"
+atomic --tools read,grep,find,ls -p "Review the code"
 ```
 
 ### Environment Variables
 
 | Variable | Description |
 |----------|-------------|
-| `PI_CODING_AGENT_DIR` | Override config directory; default is `~/.pi/agent` |
-| `PI_CODING_AGENT_SESSION_DIR` | Override session storage directory; overridden by `--session-dir` |
-| `PI_PACKAGE_DIR` | Override package directory, useful for Nix/Guix store paths |
-| `PI_OFFLINE` | Disable startup network operations, including update checks, package update checks, and install/update telemetry |
-| `PI_SKIP_VERSION_CHECK` | Skip the Pi version update check at startup. This prevents the `pi.dev` latest-version request |
-| `PI_TELEMETRY` | Override install/update telemetry: `1`/`true`/`yes` or `0`/`false`/`no`. This does not disable update checks |
-| `PI_CACHE_RETENTION` | Set to `long` for extended prompt cache where supported |
+| `ATOMIC_CODING_AGENT_DIR` | Override config directory; default is `~/.atomic/agent` |
+| `ATOMIC_CODING_AGENT_SESSION_DIR` | Override session storage directory; overridden by `--session-dir` |
+| `ATOMIC_PACKAGE_DIR` | Override package directory, useful for Nix/Guix store paths |
+| `ATOMIC_OFFLINE` | Disable startup network operations, including update checks, package update checks, and install/update telemetry |
+| `ATOMIC_SKIP_VERSION_CHECK` | Skip the Atomic version update check at startup. This prevents the latest-version request |
+| `ATOMIC_TELEMETRY` | Override install/update telemetry: `1`/`true`/`yes` or `0`/`false`/`no`. This does not disable update checks |
+| `PI_CACHE_RETENTION` | Provider/upstream-specific prompt-cache retention knob; set to `long` where supported |
 | `VISUAL`, `EDITOR` | External editor for CTRL+G |
 
-## Design Principles
+`PI_*` aliases are also supported for app-specific `ATOMIC_*` variables for legacy compatibility. `PI_CACHE_RETENTION` is not one of those aliases and has no `ATOMIC_*` equivalent. Use `PI_CACHE_RETENTION=long` when configuring prompt-cache retention for providers/upstreams that support long-lived caches.
 
-Pi keeps the core small and pushes workflow-specific behavior into extensions, skills, prompt templates, and packages.
+## Design Principles
 
-It intentionally does not include built-in MCP, sub-agents, permission popups, plan mode, to-dos, or background bash. You can build or install those workflows as extensions or packages, or use external tools such as containers and tmux.
+Atomic keeps the core CLI small, while this distribution bundles first-party package extensions for workflows, subagents, MCP, web access, and intercom. Other workflows can still be installed as extensions or packages, or handled externally with tools such as containers and tmux.
 
 For the full rationale, read the [blog post](https://mariozechner.at/posts/2025-11-30-pi-coding-agent/).

package/docs/windows.md

@@ -1,8 +1,8 @@
 # Windows Setup
 
-Pi requires a bash shell on Windows. Checked locations (in order):
+Atomic requires a bash shell on Windows. Checked locations (in order):
 
-1. Custom path from `~/.pi/agent/settings.json`
+1. Custom path from `~/.atomic/agent/settings.json` (legacy `~/.pi/agent/settings.json` also supported)
 2. Git Bash (`C:\Program Files\Git\bin\bash.exe`)
 3. `bash.exe` on PATH (Cygwin, MSYS2, WSL)