diff --git a/.github/workflows/claude-code-review.yml b/.github/workflows/claude-code-review.yml
index 8452b0f2..ca92885d 100644
--- a/.github/workflows/claude-code-review.yml
+++ b/.github/workflows/claude-code-review.yml
@@ -21,7 +21,7 @@ jobs:
     runs-on: ubuntu-latest
     permissions:
       contents: read
-      pull-requests: read
+      pull-requests: write
       issues: read
       id-token: write
 
diff --git a/.github/workflows/claude.yml b/.github/workflows/claude.yml
index d300267f..4f24565f 100644
--- a/.github/workflows/claude.yml
+++ b/.github/workflows/claude.yml
@@ -20,8 +20,8 @@ jobs:
     runs-on: ubuntu-latest
     permissions:
       contents: read
-      pull-requests: read
-      issues: read
+      pull-requests: write
+      issues: write
       id-token: write
       actions: read # Required for Claude to read CI results on PRs
     steps:
diff --git a/CLAUDE.md b/CLAUDE.md
index 69f64c3c..8cd1fcf6 100644
--- a/CLAUDE.md
+++ b/CLAUDE.md
@@ -4,7 +4,7 @@ This file provides guidance to Claude Code (claude.ai/code) when working with co
 
 ## Repository Overview
 
-This is a minimal macOS dotfiles repository for zsh, git, vim, and tmux. The structure is flat with all configuration files in the root directory. External themes are managed as git submodules in `vendor/`.
+This is a minimal macOS dotfiles repository for zsh, git, vim, and tmux. Syncable dotfiles live in `home/` and are copied to `~` on install. External themes are managed as git submodules in `vendor/`.
 
 ## Installation and Updates
 
@@ -46,40 +46,39 @@ The `.zshrc` file sources other configuration files in this order:
 
 ### Key Components
 
-**Prompt System** (.zsh_prompt:23-40)
+**Prompt System** (home/.zsh_prompt:23-40)
 - Uses zsh hooks (`preexec` and `precmd`) to track command execution time
 - `preexec` captures start time before command runs
 - `precmd` calculates elapsed time after command completes
 - Timer only displayed if command takes >0 seconds
 
-**Bootstrap Process** (bootstrap.sh:76-112)
-- Uses `rsync` to sync dotfiles to home directory
-- Excludes git metadata, scripts, documentation, LaunchAgents, vendor, and preferences from sync
+**Bootstrap Process** (bootstrap.sh:76-100)
+- Uses `rsync` to sync `home/` directory contents to `~`
 - Installs tmux plugin manager (TPM) if not present
 - TPM must be manually activated in tmux with `prefix + I` after first install
 - Symlinks btop themes from `vendor/btop-catppuccin/` to `~/.config/btop/themes/`
 - Installs LaunchAgents (if dependencies are available)
 
-**Tmux Configuration** (.tmux.conf)
+**Tmux Configuration** (home/.tmux.conf)
 - Uses Catppuccin theme (mocha flavor) for status bar styling
 - Custom key bindings: `|` for horizontal split, `-` for vertical split
 - Vim-style pane navigation with Ctrl-hjkl
 - Session resurrection with `prefix + S` (save) and `prefix + Y` (restore)
 - Auto-saves sessions every 15 minutes via tmux-continuum
 
-**Git Configuration** (.gitconfig)
+**Git Configuration** (home/.gitconfig)
 - Common aliases: `st`, `co`, `br`, `ci`, `lg`, `amend`, `unstage`, `discard`
 - Auto setup remote on push, prune on fetch
 - Default branch set to `main`
 - Uses GitHub CLI (`gh`) for credential management
 
-**Vim Configuration** (.vimrc)
+**Vim Configuration** (home/.vimrc)
 - 2-space indentation with spaces (expandtab)
 - Incremental, case-smart search with highlighting
 - No swap/backup files
 - Line numbers and always-visible status line
 
-**Dark Mode Theme Switching** (.bin/toggle-btop-theme)
+**Dark Mode Theme Switching** (home/.bin/toggle-btop-theme)
 - Automatically switches btop theme based on macOS appearance
 - Uses catppuccin_mocha for dark mode, catppuccin_latte for light mode
 - Requires `dark-notify` (`brew install cormacrelf/tap/dark-notify`)
@@ -97,4 +96,4 @@ The `.zshrc` file sources other configuration files in this order:
 
 ## Personal Customizations
 
-Users can create `~/.extra` (not tracked) to add personal settings that override defaults. This file is sourced last in .zshrc:71-73.
+Users can create `~/.extra` (not tracked) to add personal settings that override defaults. This file is sourced last in home/.zshrc:71-73.
diff --git a/README.md b/README.md
index 786ab2ca..38162b4e 100644
--- a/README.md
+++ b/README.md
@@ -1,66 +1,85 @@
 # Evan's dotfiles
 
-Minimal zsh configuration for macOS.
+Minimal macOS dotfiles for zsh, git, vim, and tmux with automatic dark/light mode theme switching.
 
 ## What's included
 
-- **Zsh configuration** - History management, completion caching, directory navigation
-- **Custom prompt** - Shows directory, current time, and elapsed time for commands
-- **Basic aliases** - Navigation shortcuts and colored ls/grep
-- **PATH setup** - Adds `~/.local/bin` to PATH
-- **Tmux config** - Basic tmux setup with plugin manager
+- **Zsh** - History management, completion caching, directory navigation, custom prompt with command timer
+- **Git** - Sensible defaults, common aliases (`st`, `co`, `br`, `lg`, etc.)
+- **Vim** - 2-space indentation, Catppuccin theme, sensible search settings
+- **Tmux** - Catppuccin theme, vim-style navigation, session persistence
+- **btop** - Automatic dark/light theme switching via macOS appearance
+- **iTerm2** - Catppuccin color schemes (manual import required)
 
 ## Installation
 
-Clone the repository and run the bootstrap script:
+Clone with submodules and run bootstrap:
 
 ```bash
-git clone https://github.com/evansenter/dotfiles.git
+git clone --recursive https://github.com/evansenter/dotfiles.git
 cd dotfiles
 ./bootstrap.sh
 ```
 
-The script will sync dotfiles to your home directory. Restart your terminal or run `source ~/.zshrc` to apply changes.
+Restart your terminal or run `source ~/.zshrc` to apply changes.
+
+### Optional: Dark mode theme switching
+
+For automatic btop theme switching based on macOS appearance:
+
+```bash
+brew install cormacrelf/tap/dark-notify
+./bootstrap.sh  # Re-run to install LaunchAgent
+```
 
 ## Updating
 
-To pull the latest changes and sync:
+Pull latest and sync:
 
 ```bash
 cd dotfiles
+git pull
+git submodule update --init --remote
 ./bootstrap.sh -f
 ```
 
 ## Uninstalling
 
-To remove all dotfiles from your home directory:
-
 ```bash
 cd dotfiles
 ./uninstall.sh
 ```
 
+## Structure
+
+```
+dotfiles/
+├── home/           # Synced to ~/ on install
+│   ├── .aliases
+│   ├── .bin/
+│   ├── .exports
+│   ├── .gitconfig
+│   ├── .tmux.conf
+│   ├── .vim/
+│   ├── .vimrc
+│   ├── .zsh_prompt
+│   └── .zshrc
+├── vendor/         # Git submodules (themes)
+├── preferences/    # App config backups
+├── LaunchAgents/   # macOS LaunchAgent templates
+└── bootstrap.sh
+```
+
 ## Customization
 
-Create a `~/.extra` file (not tracked by this repo) to add personal customizations without forking:
+Create `~/.extra` (not tracked) for personal settings:
 
 ```bash
-# ~/.extra example
+# ~/.extra
 export CUSTOM_VAR="value"
 alias myalias="some command"
 ```
 
-## Features
-
-**Smart history search**: Type a command prefix (like `git`) and press ↑/↓ arrows to search matching commands in history.
-
-**Command timer**: The prompt shows how long the previous command took to run.
-
-**Clean prompt format**:
-```
-~/path/to/directory 14:32:45 3s →
-```
-
 ## Credits
 
 Based on [Mathias Bynens' dotfiles](https://github.com/mathiasbynens/dotfiles), heavily simplified.
diff --git a/bootstrap.sh b/bootstrap.sh
index c13de800..a6211871 100755
--- a/bootstrap.sh
+++ b/bootstrap.sh
@@ -8,7 +8,7 @@
 cd "$(dirname "${BASH_SOURCE}")";
 
 # Pull latest changes from remote
-git pull origin master;
+git pull origin main;
 
 # ==============================================================================
 # Functions
@@ -74,26 +74,15 @@ install_btop_themes() {
 }
 
 sync_dotfiles() {
-	# Sync dotfiles to home directory
+	# Sync dotfiles from home/ directory to ~
 	rsync \
 		--exclude ".DS_Store" \
-		--exclude ".git/" \
-		--exclude ".gitignore" \
-		--exclude ".claude/" \
-		--exclude "CLAUDE.md" \
-		--exclude "bootstrap.sh" \
-		--exclude "uninstall.sh" \
-		--exclude "LICENSE-MIT.txt" \
-		--exclude "README.md" \
-		--exclude "LaunchAgents/" \
-		--exclude "vendor/" \
-		--exclude "preferences/" \
 		--archive \
 		--verbose \
 		--human-readable \
 		--force \
 		--no-perms \
-		. ~
+		home/ ~
 
 	# Install tmux plugin manager if needed
 	install_tmux_plugin_manager
diff --git a/.aliases b/home/.aliases
similarity index 100%
rename from .aliases
rename to home/.aliases
diff --git a/.bin/toggle-btop-theme b/home/.bin/toggle-btop-theme
similarity index 100%
rename from .bin/toggle-btop-theme
rename to home/.bin/toggle-btop-theme
diff --git a/.exports b/home/.exports
similarity index 100%
rename from .exports
rename to home/.exports
diff --git a/.gitconfig b/home/.gitconfig
similarity index 100%
rename from .gitconfig
rename to home/.gitconfig
diff --git a/.tmux.conf b/home/.tmux.conf
similarity index 100%
rename from .tmux.conf
rename to home/.tmux.conf
diff --git a/.vim/colors/catppuccin_mocha.vim b/home/.vim/colors/catppuccin_mocha.vim
similarity index 100%
rename from .vim/colors/catppuccin_mocha.vim
rename to home/.vim/colors/catppuccin_mocha.vim
diff --git a/.vimrc b/home/.vimrc
similarity index 100%
rename from .vimrc
rename to home/.vimrc
diff --git a/.zsh_prompt b/home/.zsh_prompt
similarity index 100%
rename from .zsh_prompt
rename to home/.zsh_prompt
diff --git a/.zshrc b/home/.zshrc
similarity index 100%
rename from .zshrc
rename to home/.zshrc