diff --git a/CLAUDE.md b/CLAUDE.md
index 6162ac0f..85627949 100644
--- a/CLAUDE.md
+++ b/CLAUDE.md
@@ -89,17 +89,17 @@ REST API at `/api/v1/`. Key endpoints:
 
 ## Authentication
 
-User-based authentication with email/password. When no users exist (fresh install), everything works without auth until the instance is initialized with `pad setup`. Once the first admin exists, all API requests require authentication.
+User-based authentication with email/password. When no users exist (fresh install), everything works without auth until the instance is initialized with `pad auth setup`. Once the first admin exists, all API requests require authentication.
 
 ```bash
 # First-time setup
-pad setup              # Create the first admin account on the server host
+pad auth setup         # Create the first admin account on the server host
 
 # Subsequent logins
-pad login              # Email + password prompt
-pad whoami             # Show current user
-pad logout             # Sign out
-pad reset-password user@example.com  # Generate reset link (admin fallback)
+pad auth login         # Email + password prompt
+pad auth whoami        # Show current user
+pad auth logout        # Sign out
+pad auth reset-password user@example.com  # Generate reset link (admin fallback)
 
 # Credentials stored in ~/.pad/credentials.json (0600 permissions)
 # CLI auto-attaches auth token to all API requests
@@ -107,10 +107,10 @@ pad reset-password user@example.com  # Generate reset link (admin fallback)
 
 ### Workspace membership
 ```bash
-pad members                         # List workspace members
-pad invite user@example.com         # Invite (adds directly if user exists, creates join code if not)
-pad invite user@example.com --role viewer  # Invite with specific role
-pad join <code>                     # Accept a workspace invitation
+pad workspace members                         # List workspace members
+pad workspace invite user@example.com         # Invite (adds directly if user exists, creates join code if not)
+pad workspace invite user@example.com --role viewer  # Invite with specific role
+pad workspace join <code>                     # Accept a workspace invitation
 ```
 
 Roles: `owner` (full access), `editor` (CRUD items), `viewer` (read-only).
@@ -132,41 +132,41 @@ Items are referenced by **issue ID** (e.g. `TASK-5`, `BUG-8`) wherever a `<ref>`
 Slugs also work but issue IDs are preferred.
 
 ```bash
-pad create <collection> "title" [--status X] [--priority X]
-pad list [collection] [--status X] [--all]
-pad show <ref>                # e.g. pad show TASK-5
-pad update <ref> [--status X] [--priority X]
-pad delete <ref>
-pad move <ref> <target-collection>
-pad search "query"
-pad status                    # Project dashboard
-pad next                      # Recommended next task
-pad standup [--days N]        # Daily standup report
-pad changelog [--days N]      # Release notes from completed items
-pad blocks <source> <target>  # e.g. pad blocks TASK-5 TASK-8
-pad blocked-by <item> <blocker>
-pad deps <ref>                # Show dependencies
-pad unblock <source> <target>
-pad collections               # List collections
-pad collections create "Name" --fields "key:type[:opts]; ..."
-pad edit <ref>                # Open in $EDITOR
-pad init [--template X]       # Create workspace
-pad install [tool]            # Install /pad skill for AI tools
-pad onboard                   # Analyze codebase, suggest conventions
-pad open                      # Open web UI in browser
-pad watch                     # Real-time activity stream
+pad item create <collection> "title" [--status X] [--priority X]
+pad item list [collection] [--status X] [--all]
+pad item show <ref>           # e.g. pad item show TASK-5
+pad item update <ref> [--status X] [--priority X]
+pad item delete <ref>
+pad item move <ref> <target-collection>
+pad item search "query"
+pad project dashboard         # Project dashboard
+pad project next              # Recommended next task
+pad project standup [--days N]  # Daily standup report
+pad project changelog [--days N]  # Release notes from completed items
+pad item block <source> <target>  # e.g. pad item block TASK-5 TASK-8
+pad item blocked-by <item> <blocker>
+pad item deps <ref>           # Show dependencies
+pad item unblock <source> <target>
+pad collection list           # List collections
+pad collection create "Name" --fields "key:type[:opts]; ..."
+pad item edit <ref>           # Open in $EDITOR
+pad workspace init [--template X]  # Create workspace
+pad agent install [tool]      # Install /pad skill for AI tools
+pad workspace onboard         # Analyze codebase, suggest conventions
+pad server open               # Open web UI in browser
+pad project watch             # Real-time activity stream
 pad github link [item-ref]    # Link current branch's PR to item
 pad github status [item-ref]  # Show PR status for linked items
 pad github unlink <item-ref>  # Remove PR link from item
-pad bulk-update --status done TASK-5 TASK-8  # Batch operations
-pad webhooks list/create/delete/test         # Webhook management
-pad setup                     # Initialize a fresh instance with the first admin
-pad login                     # Log in
-pad logout                    # Sign out
-pad whoami                    # Show current user
-pad members                   # List workspace members
-pad invite <email> [--role X] # Invite user to workspace
-pad join <code>               # Accept workspace invitation
+pad item bulk-update --status done TASK-5 TASK-8  # Batch operations
+pad webhook list/create/delete/test               # Webhook management
+pad auth setup                # Initialize a fresh instance with the first admin
+pad auth login                # Log in
+pad auth logout               # Sign out
+pad auth whoami               # Show current user
+pad workspace members         # List workspace members
+pad workspace invite <email> [--role X] # Invite user to workspace
+pad workspace join <code>     # Accept workspace invitation
 ```
 
 Collection names accept singular forms: `task`→`tasks`, `idea`→`ideas`, `doc`→`docs`.
@@ -177,7 +177,7 @@ Collection names accept singular forms: `task`→`tasks`, `idea`→`ideas`, `doc
 - **Items** have structured `fields` JSON + optional rich `content` (markdown)
 - **Wiki-links** `[[Title]]` resolve across all items, rendered as clickable links
 - **Default collections:** Tasks, Ideas, Phases, Docs
-- **Templates:** startup (default), scrum, product — set via `pad init --template`
+- **Templates:** startup (default), scrum, product — set via `pad workspace init --template`
 
 ## Testing
 
diff --git a/Makefile b/Makefile
index 9bd90ab6..fcec4c01 100644
--- a/Makefile
+++ b/Makefile
@@ -25,24 +25,24 @@ install: build
 	rm -f ~/.pad/pad.pid
 	@echo "Installed $(BINARY) to $(INSTALL_DIR)/$(BINARY)"
 	@# Trigger server auto-start by running a command
-	@$(INSTALL_DIR)/$(BINARY) status 2>/dev/null || true
+	@$(INSTALL_DIR)/$(BINARY) auth whoami 2>/dev/null || true
 	@echo "Server restarted."
 
 test:
 	go test ./... -v
 
 dev: build-go
-	./$(BINARY) serve --host $(HOST)
+	./$(BINARY) server start --host $(HOST)
 
 serve: build
-	-./$(BINARY) stop 2>/dev/null
+	-./$(BINARY) server stop 2>/dev/null
 	@sleep 1
-	./$(BINARY) serve --host $(HOST)
+	./$(BINARY) server start --host $(HOST)
 
 restart: build-go
-	-./$(BINARY) stop 2>/dev/null
+	-./$(BINARY) server stop 2>/dev/null
 	@sleep 1
-	./$(BINARY) serve --host $(HOST)
+	./$(BINARY) server start --host $(HOST)
 
 web:
 	cd web && npm ci && npm run build
diff --git a/README.md b/README.md
index 403419de..4867e858 100644
--- a/README.md
+++ b/README.md
@@ -25,12 +25,12 @@
 ```bash
 brew install xarmian/tap/pad
 cd your-project
-pad configure
-pad init
-pad open
+pad auth configure
+pad workspace init
+pad server open
 ```
 
-For a local install, choose `Local` in `pad configure`. Pad will remember that this client manages a local server, auto-start it when needed, and open the web UI at `localhost:7777`.
+For a local install, choose `Local` in `pad auth configure`. Pad will remember that this client manages a local server, auto-start it when needed, and open the web UI at `localhost:7777`.
 
 ## Why Pad?
 
@@ -38,7 +38,7 @@ Tools like Linear, Jira, and Notion are built for teams on the cloud. Pad is bui
 
 | | Pad | Linear / Jira | Notion |
 |---|---|---|---|
-| **Setup** | `pad configure` + `pad init` | Create account, invite team, configure | Create account, pick template |
+| **Setup** | `pad auth configure` + `pad workspace init` | Create account, invite team, configure | Create account, pick template |
 | **AI agents** | Native `/pad` skill for 7+ tools | Third-party integrations | Third-party integrations |
 | **Data** | Local SQLite, you own it | Their cloud | Their cloud |
 | **Offline** | Full functionality | Read-only cache at best | Limited |
@@ -52,12 +52,12 @@ Tools like Linear, Jira, and Notion are built for teams on the cloud. Pad is bui
 **CLI that doesn't get in your way.** Create tasks, search items, check status — without leaving the terminal.
 
 ```bash
-pad create task "Fix OAuth redirect" --priority high
-pad create idea "Real-time collaboration" --category infrastructure
-pad list tasks --status in-progress
-pad search "authentication"
-pad status                              # Project dashboard
-pad next                                # What should I work on?
+pad item create task "Fix OAuth redirect" --priority high
+pad item create idea "Real-time collaboration" --category infrastructure
+pad item list tasks --status in-progress
+pad item search "authentication"
+pad project dashboard                   # Project dashboard
+pad project next                        # What should I work on?
 ```
 
 **Web UI that stays out of your way.** A clean, dark-themed interface at `localhost:7777` with:
@@ -76,7 +76,7 @@ pad next                                # What should I work on?
 **Your agent becomes a project partner.** Install the `/pad` skill once, and your AI coding tool can read, create, and update project items through natural language.
 
 ```bash
-pad install              # Auto-detects your tools and installs the skill
+pad agent install        # Auto-detects your tools and installs the skill
 ```
 
 Works with **Claude Code**, **Cursor**, **Windsurf**, **Codex**, **GitHub Copilot**, **Amazon Q**, and **JetBrains Junie**.
@@ -96,7 +96,7 @@ Then just talk to your project:
 - **Playbooks** — multi-step workflows like "when implementing a feature: read the spec, create a branch, write tests first, then implement"
 
 ```bash
-pad create convention "Run tests before completing tasks" \
+pad item create convention "Run tests before completing tasks" \
   --field trigger=on-task-complete \
   --field scope=all \
   --field priority=must
@@ -107,7 +107,7 @@ Agents load relevant conventions automatically. All agent actions are attributed
 **Onboard agents to a new codebase:**
 
 ```bash
-pad onboard              # Analyzes project structure and suggests conventions
+pad workspace onboard    # Analyzes project structure and suggests conventions
 ```
 
 ### Collections & Custom Fields
@@ -128,7 +128,7 @@ Pad organizes work into **collections** — typed containers with structured fie
 **Create your own** with typed fields — select, text, date, number, url, relation, checkbox:
 
 ```bash
-pad collections create "Bug Reports" \
+pad collection create "Bug Reports" \
   --fields "severity:select:low,medium,high,critical; browser:text; reproducible:checkbox"
 ```
 
@@ -180,7 +180,7 @@ Pre-built binaries for macOS, Linux, and Windows are available on the [releases
 ### 1. Configure this Pad client
 
 ```bash
-pad configure
+pad auth configure
 ```
 
 For most local installs, choose `Local`. If you're connecting to another Pad server, choose `Remote` or `Docker` and enter its base URL.
@@ -189,35 +189,35 @@ For most local installs, choose `Local`. If you're connecting to another Pad ser
 
 ```bash
 cd ~/projects/myapp
-pad init "My App"
+pad workspace init "My App"
 ```
 
 This creates a `.pad.toml` file linking your project directory to a Pad workspace with default collections. Choose a template to start with pre-configured collections:
 
 ```bash
-pad init "My App" --template scrum     # Scrum-style with sprints
-pad init "My App" --template product   # Product management focused
+pad workspace init "My App" --template scrum     # Scrum-style with sprints
+pad workspace init "My App" --template product   # Product management focused
 ```
 
 ### 3. Install the AI skill
 
 ```bash
-pad install                  # Auto-detect and install for all found tools
-pad install claude           # Or install for a specific tool
-pad install cursor
-pad install copilot
+pad agent install            # Auto-detect and install for all found tools
+pad agent install claude     # Or install for a specific tool
+pad agent install cursor
+pad agent install copilot
 ```
 
 ### 4. Start working
 
 ```bash
 # From the CLI
-pad create task "Set up CI pipeline" --priority high
-pad create idea "Add WebSocket support" --category infrastructure
-pad status
+pad item create task "Set up CI pipeline" --priority high
+pad item create idea "Add WebSocket support" --category infrastructure
+pad project dashboard
 
 # From the web UI
-pad open                     # Opens localhost:7777 in your browser
+pad server open              # Opens localhost:7777 in your browser
 
 # From your AI agent
 # Just use /pad in Claude Code, Cursor, etc.
@@ -226,86 +226,101 @@ pad open                     # Opens localhost:7777 in your browser
 ### 5. Teach your agents the rules
 
 ```bash
-pad onboard                  # Auto-analyze project and suggest conventions
+pad workspace onboard        # Auto-analyze project and suggest conventions
 # Or browse the convention library
-pad library conventions      # Pre-built conventions you can adopt
-pad library playbooks        # Pre-built multi-step workflows
+pad library list --type conventions  # Pre-built conventions you can adopt
+pad library list --type playbooks    # Pre-built multi-step workflows
 ```
 
 ## CLI Reference
 
 ```
-pad configure                 Configure how this client connects to Pad
-pad init [name]              Initialize workspace in current directory
-pad open                     Open web UI in browser
-pad install [tool]           Install /pad skill for AI coding tools
-pad onboard                  Analyze project and suggest conventions
+pad auth configure                    Configure how this client connects to Pad
+pad auth setup                        Initialize the first admin account
+pad auth login                        Sign in
+pad auth whoami                       Show current user
 
-pad create <coll> "title"    Create item (task, idea, phase, doc, ...)
-pad list [collection]        List items (filters: --status, --priority, --all)
-pad show <slug>              Show item detail
-pad update <slug>            Update item fields
-pad delete <slug>            Delete item
-pad move <slug> <collection> Move item between collections
-pad edit <slug>              Open item in $EDITOR
-pad search "query"           Full-text search across all items
+pad server start                      Start the Pad API server
+pad server stop                       Stop the Pad server
+pad server open                       Open web UI in browser
 
-pad status                   Project dashboard
-pad next                     Recommended next task
-pad ready                    Query actionable next items
-pad stale                    Query stalled or attention-worthy items
-pad related <ref>            Show direct relationships for an item
-pad implemented-by <ref>     Show incoming implementers for an item
-pad collections              List collections with item counts
-pad comment <slug> "text"    Add comment to an item
-pad comments <slug>          View item comments
-pad note <ref> "summary"     Append an implementation note to an item
-pad decide <ref> "decision"  Append a decision log entry to an item
+pad workspace init [name]             Initialize workspace in current directory
+pad workspace link <workspace>        Link current directory to an existing workspace
+pad workspace list                    List all workspaces
+pad workspace switch <workspace>      Switch active workspace
+pad workspace onboard                 Analyze project and suggest conventions
+pad workspace members                 List workspace members
+pad workspace invite <email>          Invite a workspace member
+pad workspace join <code>             Accept an invitation
+pad workspace export                  Export workspace data
+pad workspace import <file>           Import workspace data
 
-pad standup [--days N]        Daily standup report
-pad changelog [--days N]     Release notes from completed items
-pad watch                    Real-time activity stream
+pad project dashboard                 Project dashboard
+pad project next                      Recommended next task
+pad project ready                     Query actionable next items
+pad project stale                     Query stalled or attention-worthy items
+pad project standup [--days N]        Daily standup report
+pad project changelog [--days N]      Release notes from completed items
+pad project watch                     Real-time activity stream
+pad project reconcile                 Reconcile item and PR state
 
-pad blocks <src> <target>    Create dependency
-pad blocked-by <item> <blk>  Mark item as blocked
-pad deps <slug>              Show dependencies
-pad unblock <src> <target>   Remove dependency
+pad item create <coll> "title"        Create item (task, idea, phase, doc, ...)
+pad item list [collection]            List items (filters: --status, --priority, --all)
+pad item show <ref>                   Show item detail
+pad item update <ref>                 Update item fields
+pad item delete <ref>                 Delete item
+pad item move <ref> <collection>      Move item between collections
+pad item edit <ref>                   Open item in $EDITOR
+pad item search "query"               Full-text search across all items
+pad item comment <ref> "text"         Add comment to an item
+pad item comments <ref>               View item comments
+pad item note <ref> "summary"         Append an implementation note to an item
+pad item decide <ref> "decision"      Append a decision log entry to an item
+pad item block <src> <target>         Create dependency
+pad item blocked-by <item> <blk>      Mark item as blocked
+pad item deps <ref>                   Show dependencies
+pad item unblock <src> <target>       Remove dependency
+pad item related <ref>                Show direct relationships for an item
+pad item implemented-by <ref>         Show incoming implementers for an item
+pad item bulk-update --status X       Batch update multiple items
+
+pad collection list                   List collections with item counts
+pad collection create <name>          Create a custom collection
+
+pad library list                      Browse convention and playbook library
+pad library activate <title>          Activate a convention or playbook
+
+pad agent install [tool]              Install /pad skill for AI coding tools
+pad agent status                      Show supported tools and installation status
+pad agent update                      Update installed tool integrations
 
 pad github link [item-ref]   Link current branch's PR to item
 pad github status [item-ref] Show PR status for linked items
 pad github unlink <item-ref> Remove PR link from item
 
-pad webhooks list            List workspace webhooks
-pad webhooks create <url>    Create webhook
-pad bulk-update --status X   Batch update multiple items
-
-pad export                   Export workspace data
-pad import <file>            Import workspace data
-
-pad workspaces               List all workspaces
-pad switch <workspace>       Switch active workspace
-pad library [type]           Browse convention and playbook library
+pad webhook list             List workspace webhooks
+pad webhook create <url>     Create webhook
 ```
 
 All commands accept `--format json` for machine-readable output and `--workspace` to target a specific workspace.
 
 ### Authentication
 
-Pad runs without authentication by default for frictionless local use. On a fresh instance, run `pad setup` on the server host to create the first admin account:
+Pad runs without authentication by default for frictionless local use. On a fresh instance, run `pad auth setup` on the server host to create the first admin account:
 
 ```bash
-pad setup              # Initialize the first admin account
-pad login              # Sign in
-pad whoami             # Show current user
-pad logout             # Sign out
+pad auth setup         # Initialize the first admin account
+pad auth login         # Sign in
+pad auth whoami        # Show current user
+pad auth logout        # Sign out
 ```
 
 Once a user exists, all API requests and web UI access require authentication. Credentials are stored in `~/.pad/credentials.json`. Multiple users can be invited to workspaces with role-based access control (`owner`, `editor`, `viewer`).
 
 ```bash
-pad members                         # List workspace members
-pad invite user@example.com         # Invite to workspace
-pad join <code>                     # Accept invitation
+pad workspace members               # List workspace members
+pad workspace invite user@example.com
+pad workspace join <code>
 ```
 
 ## Architecture
diff --git a/cmd/pad/configure.go b/cmd/pad/configure.go
index eabfef32..9aa053ae 100644
--- a/cmd/pad/configure.go
+++ b/cmd/pad/configure.go
@@ -63,7 +63,7 @@ func getConfiguredConfig() *config.Config {
 	}
 
 	if !canPromptForConfig() {
-		fmt.Fprintln(os.Stderr, "Pad is not configured. Run 'pad configure' first.")
+		fmt.Fprintln(os.Stderr, "Pad is not configured. Run 'pad auth configure' first.")
 		os.Exit(1)
 	}
 
@@ -77,7 +77,7 @@ func getConfiguredConfig() *config.Config {
 
 	cfg = getConfig()
 	if !cfg.IsConfigured() {
-		fmt.Fprintln(os.Stderr, "Error: Pad configuration was not saved. Run 'pad configure' again.")
+		fmt.Fprintln(os.Stderr, "Error: Pad configuration was not saved. Run 'pad auth configure' again.")
 		os.Exit(1)
 	}
 	return cfg
diff --git a/cmd/pad/groups.go b/cmd/pad/groups.go
new file mode 100644
index 00000000..82a2bf97
--- /dev/null
+++ b/cmd/pad/groups.go
@@ -0,0 +1,162 @@
+package main
+
+import "github.com/spf13/cobra"
+
+func authCmd() *cobra.Command {
+	cmd := &cobra.Command{
+		Use:   "auth",
+		Short: "Configure authentication and account access",
+	}
+	cmd.AddCommand(
+		configureCmd(),
+		setupCmd(),
+		loginCmd(),
+		logoutCmd(),
+		whoamiCmd(),
+		resetPasswordCmd(),
+	)
+	return cmd
+}
+
+func serverCmd() *cobra.Command {
+	cmd := &cobra.Command{
+		Use:   "server",
+		Short: "Manage the Pad server process and web UI",
+	}
+	cmd.AddCommand(
+		serveCmd(),
+		stopCmd(),
+		openCmd(),
+	)
+	return cmd
+}
+
+func workspaceCmd() *cobra.Command {
+	cmd := &cobra.Command{
+		Use:   "workspace",
+		Short: "Manage workspaces and workspace membership",
+	}
+	cmd.AddCommand(
+		initCmd(),
+		linkCmd(),
+		switchCmd(),
+		workspacesCmd(),
+		onboardCmd(),
+		membersCmd(),
+		inviteCmd(),
+		joinCmd(),
+		exportCmd(),
+		importCmd(),
+	)
+	return cmd
+}
+
+func projectCmd() *cobra.Command {
+	cmd := &cobra.Command{
+		Use:   "project",
+		Short: "Inspect project state, reports, and activity",
+	}
+	cmd.AddCommand(
+		statusCmd(),
+		nextCmd(),
+		readyCmd(),
+		staleCmd(),
+		standupCmd(),
+		changelogCmd(),
+		watchCmd(),
+		reconcileCmd(),
+	)
+	return cmd
+}
+
+func itemCmd() *cobra.Command {
+	cmd := &cobra.Command{
+		Use:   "item",
+		Short: "Create, update, relate, and discuss Pad items",
+	}
+	cmd.AddCommand(
+		createCmd(),
+		listCmd(),
+		showCmd(),
+		updateCmd(),
+		deleteCmd(),
+		moveCmd(),
+		editCmd(),
+		searchCmd(),
+		bulkUpdateCmd(),
+		commentCmd(),
+		commentsCmd(),
+		noteCmd(),
+		decideCmd(),
+		blocksCmd(),
+		blockedByCmd(),
+		depsCmd(),
+		unblockCmd(),
+		splitFromCmd(),
+		supersedesCmd(),
+		implementsCmd(),
+		unsplitCmd(),
+		unsupersedeCmd(),
+		unimplementsCmd(),
+		relatedCmd(),
+		implementedByCmd(),
+	)
+	return cmd
+}
+
+func collectionCmd() *cobra.Command {
+	cmd := &cobra.Command{
+		Use:   "collection",
+		Short: "List and create collections",
+	}
+	cmd.AddCommand(
+		collectionsCmd(),
+		collectionsCreateCmd(),
+	)
+	return cmd
+}
+
+func libraryGroupCmd() *cobra.Command {
+	cmd := &cobra.Command{
+		Use:   "library",
+		Short: "Browse and activate pre-built conventions and playbooks",
+	}
+	cmd.AddCommand(
+		libraryCmd(),
+		libraryActivateCmd(),
+	)
+	return cmd
+}
+
+func agentCmd() *cobra.Command {
+	cmd := &cobra.Command{
+		Use:   "agent",
+		Short: "Install and manage Pad agent skills",
+	}
+	cmd.AddCommand(
+		installCmd(),
+		agentUpdateCmd(),
+		agentStatusCmd(),
+	)
+	return cmd
+}
+
+func agentUpdateCmd() *cobra.Command {
+	return &cobra.Command{
+		Use:   "update",
+		Short: "Update installed Pad skills across all supported tools",
+		RunE: func(cmd *cobra.Command, args []string) error {
+			return installUpdate()
+		},
+	}
+}
+
+func agentStatusCmd() *cobra.Command {
+	return &cobra.Command{
+		Use:   "status",
+		Short: "Show installed Pad skill status across supported tools",
+		RunE: func(cmd *cobra.Command, args []string) error {
+			return installList()
+		},
+	}
+}
diff --git a/cmd/pad/lineage.go b/cmd/pad/lineage.go
index c221ee8c..10b8be1e 100644
--- a/cmd/pad/lineage.go
+++ b/cmd/pad/lineage.go
@@ -23,7 +23,7 @@ func splitFromCmd() *cobra.Command {
 
 The first item is the derived item, and the second item is the original source.
 For example:
-  pad split-from TASK-122 TASK-121`,
+  pad item split-from TASK-122 TASK-121`,
 		Args: cobra.ExactArgs(2),
 		RunE: func(cmd *cobra.Command, args []string) error {
 			return createLineageLink(lineageLinkSpec{
@@ -42,7 +42,7 @@ func supersedesCmd() *cobra.Command {
 
 The first item is the newer replacement, and the second item is the older item.
 For example:
-  pad supersedes TASK-130 TASK-118`,
+  pad item supersedes TASK-130 TASK-118`,
 		Args: cobra.ExactArgs(2),
 		RunE: func(cmd *cobra.Command, args []string) error {
 			return createLineageLink(lineageLinkSpec{
@@ -61,7 +61,7 @@ func implementsCmd() *cobra.Command {
 
 The first item is the implementation work item, and the second item is the item being implemented.
 For example:
-  pad implements TASK-121 IDEA-108`,
+  pad item implements TASK-121 IDEA-108`,
 		Args: cobra.ExactArgs(2),
 		RunE: func(cmd *cobra.Command, args []string) error {
 			return createLineageLink(lineageLinkSpec{
diff --git a/cmd/pad/main.go b/cmd/pad/main.go
index 13070663..b59d069a 100644
--- a/cmd/pad/main.go
+++ b/cmd/pad/main.go
@@ -73,66 +73,17 @@ func main() {
 	rootCmd.PersistentFlags().StringVar(&urlFlag, "url", "", "server URL override (e.g., https://api.getpad.dev)")
 
 	rootCmd.AddCommand(
-		serveCmd(),
-		stopCmd(),
-		configureCmd(),
-		setupCmd(),
-		openCmd(),
-		loginCmd(),
-		logoutCmd(),
-		whoamiCmd(),
-		initCmd(),
-		linkCmd(),
-		onboardCmd(),
-		workspacesCmd(),
-		switchCmd(),
-		skillsCmd(),
-		installCmd(),
-		completionCmd(),
-		// v2 commands
-		createCmd(),
-		listCmd(),
-		showCmd(),
-		updateCmd(),
-		deleteCmd(),
-		moveCmd(),
-		searchCmd(),
-		reconcileCmd(),
-		statusCmd(),
-		nextCmd(),
-		standupCmd(),
-		changelogCmd(),
-		collectionsCmd(),
-		editCmd(),
-		libraryCmd(),
-		readyCmd(),
-		staleCmd(),
-		relatedCmd(),
-		implementedByCmd(),
-		commentCmd(),
-		commentsCmd(),
-		noteCmd(),
-		decideCmd(),
-		blocksCmd(),
-		blockedByCmd(),
-		splitFromCmd(),
-		supersedesCmd(),
-		implementsCmd(),
-		depsCmd(),
-		unblockCmd(),
-		unsplitCmd(),
-		unsupersedeCmd(),
-		unimplementsCmd(),
-		exportCmd(),
-		importCmd(),
-		watchCmd(),
-		webhooksCmd(),
-		bulkUpdateCmd(),
+		authCmd(),
+		serverCmd(),
+		workspaceCmd(),
+		projectCmd(),
+		itemCmd(),
+		collectionCmd(),
+		libraryGroupCmd(),
+		agentCmd(),
 		githubCmd(),
-		membersCmd(),
-		inviteCmd(),
-		joinCmd(),
-		resetPasswordCmd(),
+		webhooksCmd(),
+		completionCmd(),
 	)
 
 	rootCmd.RegisterFlagCompletionFunc("workspace", func(cmd *cobra.Command, args []string, toComplete string) ([]string, cobra.ShellCompDirective) {
@@ -205,7 +156,7 @@ func serveCmd() *cobra.Command {
 	var port int
 
 	cmd := &cobra.Command{
-		Use:   "serve",
+		Use:   "start",
 		Short: "Start the Pad API server",
 		RunE: func(cmd *cobra.Command, args []string) error {
 			cfg := getConfig()
@@ -354,9 +305,9 @@ func setupCmd() *cobra.Command {
 			if cfg.IsConfigured() {
 				switch cfg.Mode {
 				case config.ModeDocker:
-					return fmt.Errorf("docker-managed Pad must be initialized from inside the container; run 'docker exec -it <container> pad setup'")
+					return fmt.Errorf("docker-managed Pad must be initialized from inside the container; run 'docker exec -it <container> pad auth setup'")
 				case config.ModeRemote, config.ModeCloud:
-					return fmt.Errorf("remote Pad instances must be initialized on the server host with 'pad setup'")
+					return fmt.Errorf("remote Pad instances must be initialized on the server host with 'pad auth setup'")
 				}
 			}
 
@@ -374,7 +325,7 @@ func setupCmd() *cobra.Command {
 					fmt.Println("Pad is already initialized and you are logged in.")
 					return nil
 				}
-				fmt.Println("Pad is already initialized. Run 'pad login' to sign in.")
+				fmt.Println("Pad is already initialized. Run 'pad auth login' to sign in.")
 				return nil
 			}
 
@@ -515,11 +466,11 @@ func printSetupRequiredHint(cfg *config.Config) {
 	fmt.Println("This Pad instance has not been initialized yet.")
 	switch cfg.Mode {
 	case config.ModeDocker:
-		fmt.Println("Run 'pad setup' inside the container, for example: docker exec -it <container> pad setup")
+		fmt.Println("Run 'pad auth setup' inside the container, for example: docker exec -it <container> pad auth setup")
 	case config.ModeRemote, config.ModeCloud:
-		fmt.Println("Run 'pad setup' on the machine or container running the Pad server, then try again.")
+		fmt.Println("Run 'pad auth setup' on the machine or container running the Pad server, then try again.")
 	default:
-		fmt.Println("Run 'pad setup' to create the first admin account, then try again.")
+		fmt.Println("Run 'pad auth setup' to create the first admin account, then try again.")
 	}
 }
 
@@ -574,7 +525,7 @@ func whoamiCmd() *cobra.Command {
 				return fmt.Errorf("load credentials: %w", err)
 			}
 			if creds == nil || creds.Token == "" {
-				fmt.Println("Not logged in. Run 'pad login'.")
+				fmt.Println("Not logged in. Run 'pad auth login'.")
 				return nil
 			}
 
@@ -587,7 +538,7 @@ func whoamiCmd() *cobra.Command {
 
 			user, err := client.GetCurrentUser()
 			if err != nil {
-				fmt.Println("Session expired. Run 'pad login'.")
+				fmt.Println("Session expired. Run 'pad auth login'.")
 				return nil
 			}
 
@@ -708,7 +659,7 @@ func inviteCmd() *cobra.Command {
 				} else {
 					code, _ := result["code"].(string)
 					fmt.Printf("  Join code: %s\n", code)
-					fmt.Printf("  They can accept with: pad join %s\n", code)
+					fmt.Printf("  They can accept with: pad workspace join %s\n", code)
 				}
 			}
 
@@ -781,7 +732,7 @@ func initCmd() *cobra.Command {
 		Long: `Create a workspace and link it to the current directory.
 
 Use --template to choose a workspace template:
-  pad init myproject --template scrum
+  pad workspace init myproject --template scrum
 
 Use --list-templates to see available templates.`,
 		Args: cobra.MaximumNArgs(1),
@@ -927,11 +878,11 @@ func linkCmd() *cobra.Command {
 		Short: "Link the current directory to an existing workspace",
 		Long: `Link the current directory to an existing workspace by creating a .pad.toml file.
 
-Unlike 'pad init', this does NOT create a new workspace — it only links to one that already exists.
+Unlike 'pad workspace init', this does NOT create a new workspace — it only links to one that already exists.
 
-  pad link myproject
+  pad workspace link myproject
 
-Use 'pad workspaces' to see available workspaces.`,
+Use 'pad workspace list' to see available workspaces.`,
 		Args: cobra.ExactArgs(1),
 		RunE: func(cmd *cobra.Command, args []string) error {
 			client, _ := getClient()
@@ -968,7 +919,7 @@ Use 'pad workspaces' to see available workspaces.`,
 				for _, w := range workspaces {
 					fmt.Fprintf(os.Stderr, "  %-20s (slug: %s)\n", w.Name, w.Slug)
 				}
-				return fmt.Errorf("workspace %q does not exist — use 'pad init %s' to create it", nameOrSlug, nameOrSlug)
+				return fmt.Errorf("workspace %q does not exist — use 'pad workspace init %s' to create it", nameOrSlug, nameOrSlug)
 			}
 
 			if err := cli.WriteWorkspaceLink(cwd, ws.Slug); err != nil {
@@ -1016,7 +967,7 @@ func offerSkillInstall() {
 				recordInstallation(tool.Name, path)
 			}
 		}
-		fmt.Printf("\n/pad skill already installed for %d tool(s). Run 'pad install --update' to update.\n", len(detected))
+		fmt.Printf("\n/pad skill already installed for %d tool(s). Run 'pad agent update' to update.\n", len(detected))
 		return
 	}
 
@@ -1055,7 +1006,7 @@ func offerSkillInstall() {
 
 	choice := readChoice()
 	if choice == "n" || choice == "N" {
-		fmt.Println("Skipped. Run 'pad install' later.")
+		fmt.Println("Skipped. Run 'pad agent install' later.")
 		return
 	}
 
@@ -1099,7 +1050,7 @@ func printOnboardingHints() {
 	fmt.Printf("  %s  %s\n", cyan.Sprint("/pad"), "create a phase for what I'm working on")
 	fmt.Println()
 	fmt.Printf("Or open the web UI at %s\n", bold.Sprint("http://localhost:7777"))
-	fmt.Println(dim.Sprint("Run 'pad status' to see your project dashboard"))
+	fmt.Println(dim.Sprint("Run 'pad project dashboard' to see your project dashboard"))
 }
 
 // --- onboard ---
@@ -1187,7 +1138,7 @@ recommend conventions from the built-in library.`,
 			if !cli.IsTerminal() {
 				// Non-interactive: just print suggestions
 				fmt.Println()
-				fmt.Println("Run 'pad onboard' in a terminal to activate, or use:")
+				fmt.Println("Run 'pad workspace onboard' in a terminal to activate, or use:")
 				fmt.Println("  /pad what conventions should this project follow?")
 				return nil
 			}
@@ -1242,53 +1193,6 @@ recommend conventions from the built-in library.`,
 	return cmd
 }
 
-// --- skills ---
-
-func skillsCmd() *cobra.Command {
-	cmd := &cobra.Command{
-		Use:   "skills",
-		Short: "Manage skill installation (use 'pad install' for multi-tool support)",
-	}
-
-	installCmd := &cobra.Command{
-		Use:   "install",
-		Short: "Install Claude Code skills",
-		RunE: func(cmd *cobra.Command, args []string) error {
-			global, _ := cmd.Flags().GetBool("global")
-			target := "project"
-			if global {
-				target = "global"
-			}
-			path, err := cli.InstallSkill(pad.PadSkill, target)
-			if err != nil {
-				return err
-			}
-			fmt.Printf("Installed /pad skill to %s\n", path)
-			return nil
-		},
-	}
-	installCmd.Flags().Bool("global", false, "install to ~/.claude/skills/")
-
-	updateCmd := &cobra.Command{
-		Use:   "update",
-		Short: "Update all installed skills across all projects",
-		RunE: func(cmd *cobra.Command, args []string) error {
-			return installUpdate()
-		},
-	}
-
-	statusSubCmd := &cobra.Command{
-		Use:   "status",
-		Short: "Show skill installation status across all projects",
-		RunE: func(cmd *cobra.Command, args []string) error {
-			return installList()
-		},
-	}
-
-	cmd.AddCommand(installCmd, updateCmd, statusSubCmd)
-	return cmd
-}
-
 // --- install ---
 
 func installCmd() *cobra.Command {
@@ -1310,11 +1214,11 @@ Supported tools:
   junie        JetBrains Junie (.junie/guidelines/)
 
 Examples:
-  pad install              # Auto-detect and install
-  pad install claude       # Install for Claude Code
-  pad install cursor       # Install for Cursor/Codex/Windsurf
-  pad install --all        # Install for all detected tools
-  pad install --list       # Show supported tools and status`,
+  pad agent install              # Auto-detect and install
+  pad agent install claude       # Install for Claude Code
+  pad agent install cursor       # Install for Cursor/Codex/Windsurf
+  pad agent install --all        # Install for all detected tools
+  pad agent status               # Show supported tools and status`,
 		ValidArgs: cli.AllToolNames(),
 		RunE: func(cmd *cobra.Command, args []string) error {
 			listFlag, _ := cmd.Flags().GetBool("list")
@@ -1409,7 +1313,7 @@ func installList() error {
 	}
 
 	if outdatedCount > 0 {
-		fmt.Printf("\n  %d installation(s) can be updated. Run 'pad install --update' to update all.\n", outdatedCount)
+		fmt.Printf("\n  %d installation(s) can be updated. Run 'pad agent update' to update all.\n", outdatedCount)
 	}
 
 	return nil
@@ -1437,7 +1341,7 @@ func installUpdate() error {
 	reg, err := cli.LoadRegistry()
 	if err != nil {
 		if localUpdated == 0 {
-			fmt.Println("No tools installed. Run 'pad install' first.")
+			fmt.Println("No tools installed. Run 'pad agent install' first.")
 		}
 		return nil
 	}
@@ -1463,7 +1367,7 @@ func installUpdate() error {
 	total := localUpdated + remoteUpdated
 	if total == 0 {
 		if localUpdated == 0 && len(reg.Installations) == 0 {
-			fmt.Println("No tools installed. Run 'pad install' first.")
+			fmt.Println("No tools installed. Run 'pad agent install' first.")
 		} else {
 			fmt.Println("All installations are up to date.")
 		}
@@ -1497,7 +1401,7 @@ func recordInstallation(toolName, skillPath string) {
 func installForTool(name string) error {
 	tool := cli.ResolveTool(name)
 	if tool == nil {
-		return fmt.Errorf("unknown tool %q. Run 'pad install --list' to see supported tools", name)
+		return fmt.Errorf("unknown tool %q. Run 'pad agent status' to see supported tools", name)
 	}
 
 	content := cli.FormatForTool(*tool, pad.PadSkill)
@@ -1574,7 +1478,7 @@ func installInteractive() error {
 	choice := readChoice()
 	if choice == "n" || choice == "N" {
 		fmt.Println()
-		fmt.Println("Install individually with: pad install <tool>")
+		fmt.Println("Install individually with: pad agent install <tool>")
 		fmt.Println("Supported tools:", strings.Join(cli.AllToolNames(), ", "))
 		return nil
 	}
@@ -1597,9 +1501,8 @@ func installInteractive() error {
 
 func workspacesCmd() *cobra.Command {
 	return &cobra.Command{
-		Use:     "workspaces",
-		Aliases: []string{"ws"},
-		Short:   "List all workspaces",
+		Use:   "list",
+		Short: "List all workspaces",
 		RunE: func(cmd *cobra.Command, args []string) error {
 			client, _ := getClient()
 			workspaces, err := client.ListWorkspaces()
@@ -1607,7 +1510,7 @@ func workspacesCmd() *cobra.Command {
 				return err
 			}
 			if len(workspaces) == 0 {
-				fmt.Println("No workspaces. Run 'pad init' to create one.")
+				fmt.Println("No workspaces. Run 'pad workspace init' to create one.")
 				return nil
 			}
 
@@ -1709,10 +1612,10 @@ func createCmd() *cobra.Command {
 		Long: `Create a new item in the specified collection.
 
 Examples:
-  pad create task "Fix OAuth redirect" --priority high
-  pad create idea "Real-time collaboration" --category infrastructure
-  pad create phase "API Redesign" --status active
-  pad create doc "Payment Architecture" --category architecture --stdin
+  pad item create task "Fix OAuth redirect" --priority high
+  pad item create idea "Real-time collaboration" --category infrastructure
+  pad item create phase "API Redesign" --status active
+  pad item create doc "Payment Architecture" --category architecture --stdin
 
 Run with --help-collections to see available collections and their status values.`,
 		ValidArgsFunction: completeCollectionNames,
@@ -1849,11 +1752,11 @@ func listCmd() *cobra.Command {
 in that collection are shown. Items with status "done" are hidden by default.
 
 Examples:
-  pad list                          # all items, all collections
-  pad list tasks                    # tasks (open + in_progress by default)
-  pad list tasks --status done      # only done tasks
-  pad list ideas --status exploring # ideas being explored
-  pad list --all                    # include done/completed items`,
+  pad item list                          # all items, all collections
+  pad item list tasks                    # tasks (open + in_progress by default)
+  pad item list tasks --status done      # only done tasks
+  pad item list ideas --status exploring # ideas being explored
+  pad item list --all                    # include done/completed items`,
 		Aliases:           []string{"ls"},
 		Args:              cobra.MaximumNArgs(1),
 		ValidArgsFunction: completeCollectionNames,
@@ -2158,9 +2061,9 @@ func updateCmd() *cobra.Command {
 Items can be referenced by issue ID (e.g. TASK-5) or slug.
 
 Examples:
-  pad update TASK-5 --status done
-  pad update PHASE-2 --status active --priority high
-  pad update DOC-3 --stdin < updated-doc.md`,
+  pad item update TASK-5 --status done
+  pad item update PHASE-2 --status active --priority high
+  pad item update DOC-3 --stdin < updated-doc.md`,
 		Args: cobra.ExactArgs(1),
 		RunE: func(cmd *cobra.Command, args []string) error {
 			client, _ := getClient()
@@ -2319,8 +2222,8 @@ Incompatible fields are dropped. Use --field to set values for target-specific f
 Items can be referenced by issue ID (e.g. TASK-5) or slug.
 
 Examples:
-  pad move BUG-3 tasks                         # Move to tasks collection
-  pad move IDEA-7 tasks --field priority=high   # Move idea to tasks with priority`,
+  pad item move BUG-3 tasks                         # Move to tasks collection
+  pad item move IDEA-7 tasks --field priority=high   # Move idea to tasks with priority`,
 		Args: cobra.ExactArgs(2),
 		RunE: func(cmd *cobra.Command, args []string) error {
 			client, _ := getClient()
@@ -2416,12 +2319,12 @@ func commentsCmd() *cobra.Command {
 
 func blocksCmd() *cobra.Command {
 	return &cobra.Command{
-		Use:   "blocks <source-ref> <target-ref>",
+		Use:   "block <source-ref> <target-ref>",
 		Short: "Mark that one item blocks another",
 		Long: `Create a blocking dependency between two items.
 
 The source item blocks the target item. For example:
-  pad blocks TASK-5 TASK-8    # TASK-5 blocks TASK-8`,
+  pad item block TASK-5 TASK-8    # TASK-5 blocks TASK-8`,
 		Args: cobra.ExactArgs(2),
 		RunE: func(cmd *cobra.Command, args []string) error {
 			client, _ := getClient()
@@ -2476,7 +2379,7 @@ func blockedByCmd() *cobra.Command {
 		Long: `Create a blocking dependency (reverse direction).
 
 The source item is blocked by the blocker item. For example:
-  pad blocked-by TASK-5 TASK-3    # TASK-5 is blocked by TASK-3`,
+  pad item blocked-by TASK-5 TASK-3    # TASK-5 is blocked by TASK-3`,
 		Args: cobra.ExactArgs(2),
 		RunE: func(cmd *cobra.Command, args []string) error {
 			client, _ := getClient()
@@ -2535,7 +2438,7 @@ Shows two sections:
   Blocked by:  items that are blocking this item
 
 Example:
-  pad deps TASK-5`,
+  pad item deps TASK-5`,
 		Args: cobra.ExactArgs(1),
 		RunE: func(cmd *cobra.Command, args []string) error {
 			client, _ := getClient()
@@ -2616,7 +2519,7 @@ func unblockCmd() *cobra.Command {
 		Long: `Remove a "blocks" relationship where source blocks target.
 
 Example:
-  pad unblock TASK-5 TASK-8    # TASK-5 no longer blocks TASK-8`,
+  pad item unblock TASK-5 TASK-8    # TASK-5 no longer blocks TASK-8`,
 		Args: cobra.ExactArgs(2),
 		RunE: func(cmd *cobra.Command, args []string) error {
 			client, _ := getClient()
@@ -2749,7 +2652,7 @@ func searchCmd() *cobra.Command {
 
 func statusCmd() *cobra.Command {
 	return &cobra.Command{
-		Use:   "status",
+		Use:   "dashboard",
 		Short: "Show project dashboard — progress, attention items, suggested next",
 		RunE: func(cmd *cobra.Command, args []string) error {
 			client, _ := getClient()
@@ -3424,10 +3327,9 @@ func collectionDefaultIcon(slug string) string {
 // --- collections ---
 
 func collectionsCmd() *cobra.Command {
-	cmd := &cobra.Command{
-		Use:     "collections",
-		Short:   "List and manage collections",
-		Aliases: []string{"coll"},
+	return &cobra.Command{
+		Use:   "list",
+		Short: "List collections with item counts",
 		RunE: func(cmd *cobra.Command, args []string) error {
 			client, _ := getClient()
 			ws := getWorkspace()
@@ -3445,9 +3347,6 @@ func collectionsCmd() *cobra.Command {
 			return nil
 		},
 	}
-
-	cmd.AddCommand(collectionsCreateCmd())
-	return cmd
 }
 
 func collectionsCreateCmd() *cobra.Command {
@@ -3469,8 +3368,8 @@ Fields DSL format: key:type[:option1,option2,...]
 Separate multiple fields with newlines or semicolons.
 
 Examples:
-  pad collections create "Bugs" --fields "status:select:new,triaged,fixing,resolved;severity:select:low,medium,high,critical;component:text"
-  pad collections create "Decisions" --icon "⚖️" --fields "status:select:proposed,accepted,rejected;impact:select:low,medium,high"`,
+  pad collection create "Bugs" --fields "status:select:new,triaged,fixing,resolved;severity:select:low,medium,high,critical;component:text"
+  pad collection create "Decisions" --icon "⚖️" --fields "status:select:proposed,accepted,rejected;impact:select:low,medium,high"`,
 		Args: cobra.ExactArgs(1),
 		RunE: func(cmd *cobra.Command, args []string) error {
 			client, _ := getClient()
@@ -3716,16 +3615,16 @@ func libraryCmd() *cobra.Command {
 	var typeFilter string
 
 	cmd := &cobra.Command{
-		Use:   "library",
-		Short: "Browse and activate pre-built conventions and playbooks",
+		Use:   "list",
+		Short: "Browse pre-built conventions and playbooks",
 		Long: `Browse the convention and playbook libraries and activate items in your workspace.
 
 Examples:
-  pad library                          # List both conventions and playbooks
-  pad library --type conventions       # List conventions only
-  pad library --type playbooks         # List playbooks only
-  pad library --category git           # Filter by category
-  pad library --format json            # JSON output
+  pad library list                     # List both conventions and playbooks
+  pad library list --type conventions  # List conventions only
+  pad library list --type playbooks    # List playbooks only
+  pad library list --category git      # Filter by category
+  pad library list --format json       # JSON output
   pad library activate "Commit after task completion"  # Activate a convention or playbook`,
 		RunE: func(cmd *cobra.Command, args []string) error {
 			client, _ := getClient()
@@ -3806,8 +3705,6 @@ Examples:
 
 	cmd.Flags().StringVar(&categoryFilter, "category", "", "filter by category")
 	cmd.Flags().StringVar(&typeFilter, "type", "", "filter by type: conventions, playbooks")
-
-	cmd.AddCommand(libraryActivateCmd())
 	return cmd
 }
 
@@ -4220,15 +4117,15 @@ func watchCmd() *cobra.Command {
 
 func webhooksCmd() *cobra.Command {
 	cmd := &cobra.Command{
-		Use:   "webhooks",
+		Use:   "webhook",
 		Short: "Manage workspace webhooks",
 		Long: `Manage webhooks that receive POST notifications when events occur.
 
 Examples:
-  pad webhooks list
-  pad webhooks create https://httpbin.org/post --events "item.created,item.updated"
-  pad webhooks delete 7fde5e41
-  pad webhooks test 7fde5e41`,
+  pad webhook list
+  pad webhook create https://httpbin.org/post --events "item.created,item.updated"
+  pad webhook delete 7fde5e41
+  pad webhook test 7fde5e41`,
 	}
 
 	cmd.AddCommand(
@@ -4329,9 +4226,9 @@ func webhooksCreateCmd() *cobra.Command {
 		Long: `Register a new webhook URL to receive event notifications.
 
 Examples:
-  pad webhooks create https://httpbin.org/post
-  pad webhooks create https://slack.com/webhook/... --events "item.created,item.updated"
-  pad webhooks create https://example.com/hook --secret "mysecret"`,
+  pad webhook create https://httpbin.org/post
+  pad webhook create https://slack.com/webhook/... --events "item.created,item.updated"
+  pad webhook create https://example.com/hook --secret "mysecret"`,
 		Args: cobra.ExactArgs(1),
 		RunE: func(cmd *cobra.Command, args []string) error {
 			client, _ := getClient()
@@ -4430,9 +4327,9 @@ func bulkUpdateCmd() *cobra.Command {
 Items can be referenced by issue ID (e.g. TASK-5) or slug.
 
 Examples:
-  pad bulk-update --status done TASK-5 TASK-8 TASK-12
-  pad bulk-update --priority high IDEA-3 IDEA-7
-  pad bulk-update --status in_progress --priority urgent TASK-1 TASK-2`,
+  pad item bulk-update --status done TASK-5 TASK-8 TASK-12
+  pad item bulk-update --priority high IDEA-3 IDEA-7
+  pad item bulk-update --status in_progress --priority urgent TASK-1 TASK-2`,
 		Args: cobra.MinimumNArgs(1),
 		RunE: func(cmd *cobra.Command, args []string) error {
 			if status == "" && priority == "" {
diff --git a/cmd/pad/query.go b/cmd/pad/query.go
index 839d2817..5dc83d1a 100644
--- a/cmd/pad/query.go
+++ b/cmd/pad/query.go
@@ -34,7 +34,7 @@ func readyCmd() *cobra.Command {
 		Short: "Show actionable next items for an agent",
 		Long: `List the items that Pad currently considers ready to work on.
 
-This is the broader query-oriented counterpart to 'pad next'. It reuses the
+This is the broader query-oriented counterpart to 'pad project next'. It reuses the
 dashboard's suggested-next logic and returns the current actionable backlog
 for active phases.`,
 		RunE: func(cmd *cobra.Command, args []string) error {
diff --git a/internal/cli/agents.go b/internal/cli/agents.go
index 78c3e64f..918e76d9 100644
--- a/internal/cli/agents.go
+++ b/internal/cli/agents.go
@@ -202,7 +202,7 @@ applyTo: "**"
 	}
 }
 
-// AllToolNames returns all valid names and aliases that can be passed to `pad install`.
+// AllToolNames returns all valid names and aliases that can be passed to `pad agent install`.
 func AllToolNames() []string {
 	var names []string
 	for _, t := range SupportedTools {
diff --git a/internal/cli/detect.go b/internal/cli/detect.go
index d1cb5eec..c7bae5fd 100644
--- a/internal/cli/detect.go
+++ b/internal/cli/detect.go
@@ -8,7 +8,7 @@ import (
 
 // ProjectInfo holds detected project metadata.
 type ProjectInfo struct {
-	Language    string   // go, node, rust, python, java, etc.
+	Language   string   // go, node, rust, python, java, etc.
 	BuildTool  string   // make, npm, cargo, pip, maven, etc.
 	TestCmd    string   // detected test command
 	HasCI      bool     // CI config detected
@@ -149,7 +149,7 @@ func SuggestedConventions(info ProjectInfo) map[string]string {
 
 	// Always suggest these general ones
 	suggestions["Commit after task completion"] = "Create a git commit with a descriptive message after completing each discrete unit of work. Reference the task slug or item number in the commit message."
-	suggestions["Update task status when starting work"] = "When starting work on a task, update its status to in-progress: `pad update <slug> --status in-progress`"
+	suggestions["Update task status when starting work"] = "When starting work on a task, update its status to in-progress: `pad item update <ref> --status in-progress`"
 
 	return suggestions
 }
diff --git a/internal/cli/server.go b/internal/cli/server.go
index 6ccb3d33..624b5733 100644
--- a/internal/cli/server.go
+++ b/internal/cli/server.go
@@ -31,7 +31,7 @@ func EnsureServer(cfg *config.Config) error {
 		return fmt.Errorf("find executable: %w", err)
 	}
 
-	cmd := exec.Command(exePath, "serve")
+	cmd := exec.Command(exePath, "server", "start")
 	setSysProcAttr(cmd)
 
 	// Redirect stdout/stderr to log file
diff --git a/internal/cli/workspace.go b/internal/cli/workspace.go
index 85264e5e..be536f3b 100644
--- a/internal/cli/workspace.go
+++ b/internal/cli/workspace.go
@@ -45,7 +45,7 @@ func DetectWorkspace(flagOverride string) (string, error) {
 		dir = parent
 	}
 
-	return "", fmt.Errorf("no workspace linked. Run 'pad init' to create one")
+	return "", fmt.Errorf("no workspace linked. Run 'pad workspace init' to create one")
 }
 
 // LoadPadToml finds and reads the nearest .pad.toml by walking up from cwd.
diff --git a/internal/collections/convention_library.go b/internal/collections/convention_library.go
index 6f1c75b1..04b58fd1 100644
--- a/internal/collections/convention_library.go
+++ b/internal/collections/convention_library.go
@@ -111,7 +111,7 @@ func ConventionLibrary() []LibraryCategory {
 			Conventions: []LibraryConvention{
 				{
 					Title:    "Update task status when starting work",
-					Content:  "When starting work on a task, update its status to in-progress: `pad update <slug> --status in-progress`",
+					Content:  "When starting work on a task, update its status to in-progress: `pad item update <ref> --status in-progress`",
 					Category: "pm",
 					Trigger:  "on-task-start",
 					Scope:    "all",
diff --git a/internal/server/handlers_auth.go b/internal/server/handlers_auth.go
index 38f519fa..999b5a44 100644
--- a/internal/server/handlers_auth.go
+++ b/internal/server/handlers_auth.go
@@ -220,7 +220,7 @@ func (s *Server) handleRegister(w http.ResponseWriter, r *http.Request) {
 	}
 
 	if count == 0 {
-		writeError(w, http.StatusForbidden, "forbidden", "This Pad instance must be initialized with pad setup")
+		writeError(w, http.StatusForbidden, "forbidden", "This Pad instance must be initialized with pad auth setup")
 		return
 	}
 
@@ -285,7 +285,7 @@ func (s *Server) handleLogin(w http.ResponseWriter, r *http.Request) {
 		return
 	}
 	if count == 0 {
-		writeError(w, http.StatusConflict, "setup_required", "This Pad instance must be initialized with pad setup")
+		writeError(w, http.StatusConflict, "setup_required", "This Pad instance must be initialized with pad auth setup")
 		return
 	}
 
diff --git a/skills/INSTALL.md b/skills/INSTALL.md
index b8f8ba42..1c59938b 100644
--- a/skills/INSTALL.md
+++ b/skills/INSTALL.md
@@ -18,19 +18,18 @@ cp pad /usr/local/bin/
 
 ```bash
 cd ~/projects/myapp
-pad init "My App"
+pad workspace init "My App"
 ```
 
-`pad init` will detect that the `/pad` skill isn't installed and offer to install it to your project or globally. You can also install manually:
+`pad workspace init` will detect that the `/pad` skill isn't installed and offer to install it for detected tools. You can also install manually:
 
 ```bash
-pad skills install           # Install to .claude/skills/ in current project
-pad skills install --global  # Install to ~/.claude/skills/ for all projects
-pad skills status            # Check if installed and up to date
-pad skills update            # Update to version bundled in binary
+pad agent install claude     # Install for Claude Code
+pad agent status             # Check installed integrations
+pad agent update             # Update the version bundled in the binary
 ```
 
-When you update the `pad` binary, run `pad skills status` to check if your installed skill is outdated. If it is, run `pad skills update` to sync it.
+When you update the `pad` binary, run `pad agent status` to check if your installed integrations are outdated. If they are, run `pad agent update` to sync them.
 
 ### 3. Use it
 
@@ -60,6 +59,6 @@ The `/pad` skill is a natural-language interface — there are no rigid commands
 ## Web UI
 
 ```bash
-pad open
+pad server open
 # or visit http://localhost:7777
 ```
diff --git a/skills/pad/SKILL.md b/skills/pad/SKILL.md
index 6b8b0a6e..5d565a47 100644
--- a/skills/pad/SKILL.md
+++ b/skills/pad/SKILL.md
@@ -24,9 +24,9 @@ There is **one command**: `/pad <anything>`. You interpret the user's intent and
 On every `/pad` invocation, start by loading workspace context:
 
 ```bash
-pad status --format json    # Project overview: collections, phases, attention, suggestions
-pad collections --format json  # Available collections with schemas
-pad list conventions --field status=active --field trigger=always --format json  # Always-on project conventions
+pad project dashboard --format json    # Project overview: collections, phases, attention, suggestions
+pad collection list --format json  # Available collections with schemas
+pad item list conventions --field status=active --field trigger=always --format json  # Always-on project conventions
 ```
 
 This tells you: what collections exist, what items are in them, what's active, what needs attention, and what project conventions to always follow.
@@ -36,7 +36,7 @@ If the conventions list includes items, treat them as project rules you must fol
 ## Parse $ARGUMENTS
 
 ### No arguments
-Show project status conversationally. Run `pad status --format json`, and present the dashboard in a friendly, readable way — highlight what's active, what needs attention, and suggest what to work on next.
+Show project status conversationally. Run `pad project dashboard --format json`, and present the dashboard in a friendly, readable way — highlight what's active, what needs attention, and suggest what to work on next.
 
 ### Natural Language Routing
 
@@ -49,15 +49,15 @@ Interpret the user's intent and route to the appropriate action. Here are common
 - "document the auth architecture" → Create a Doc item
 
 **Querying:**
-- "what's on my plate?" / "what should I work on?" → `pad next --format json`
-- "how far along are we?" / "show me status" → `pad status --format json`
-- "show me all tasks" / "list bugs" → `pad list <collection> --format json`
-- "find anything about OAuth" → `pad search "OAuth" --format json`
+- "what's on my plate?" / "what should I work on?" → `pad project next --format json`
+- "how far along are we?" / "show me status" → `pad project dashboard --format json`
+- "show me all tasks" / "list bugs" → `pad item list <collection> --format json`
+- "find anything about OAuth" → `pad item search "OAuth" --format json`
 
 **Updating:**
-- "I finished the OAuth fix" / "mark TASK-5 as done" → `pad update TASK-5 --status done`
-- "I'm starting on TASK-3" → `pad update TASK-3 --status in-progress`
-- "deprioritize IDEA-7" → `pad update IDEA-7 --priority low`
+- "I finished the OAuth fix" / "mark TASK-5 as done" → `pad item update TASK-5 --status done`
+- "I'm starting on TASK-3" → `pad item update TASK-3 --status in-progress`
+- "deprioritize IDEA-7" → `pad item update IDEA-7 --priority low`
 
 **Planning:**
 - "let's plan the next phase" → Multi-step planning workflow (see below)
@@ -69,16 +69,16 @@ Interpret the user's intent and route to the appropriate action. Here are common
 - "what if we added X?" → Discuss, then offer to capture as an Idea
 
 **Dependencies:**
-- "what's blocking TASK-5?" / "show deps for TASK-5" → `pad deps TASK-5 --format json`
-- "TASK-5 blocks TASK-8" → `pad blocks TASK-5 TASK-8`
-- "TASK-5 depends on TASK-3" → `pad blocked-by TASK-5 TASK-3`
-- "remove the dependency" → `pad unblock TASK-5 TASK-8`
+- "what's blocking TASK-5?" / "show deps for TASK-5" → `pad item deps TASK-5 --format json`
+- "TASK-5 blocks TASK-8" → `pad item block TASK-5 TASK-8`
+- "TASK-5 depends on TASK-3" → `pad item blocked-by TASK-5 TASK-3`
+- "remove the dependency" → `pad item unblock TASK-5 TASK-8`
 
 **Reports:**
-- "prep for standup" / "what did we do?" → `pad standup --format json`
-- "generate changelog" / "what shipped?" → `pad changelog --format json`
-- "changelog for this phase" → `pad changelog --phase PHASE-2 --format json`
-- "changelog since Monday" → `pad changelog --since 2026-03-24 --format json`
+- "prep for standup" / "what did we do?" → `pad project standup --format json`
+- "generate changelog" / "what shipped?" → `pad project changelog --format json`
+- "changelog for this phase" → `pad project changelog --phase PHASE-2 --format json`
+- "changelog since Monday" → `pad project changelog --since 2026-03-24 --format json`
 
 **Retrospective:**
 - "phase 2 is done, let's retro" → Review completed work, save retrospective
@@ -93,20 +93,20 @@ When you are about to take action (implement code, complete a task, create a PR,
 
 ```bash
 # Before implementing code:
-pad list conventions --field trigger=on-implement --field status=active --format json
-pad list playbooks --field trigger=on-implement --field status=active --format json
+pad item list conventions --field trigger=on-implement --field status=active --format json
+pad item list playbooks --field trigger=on-implement --field status=active --format json
 
 # Before completing a task:
-pad list conventions --field trigger=on-task-complete --field status=active --format json
+pad item list conventions --field trigger=on-task-complete --field status=active --format json
 
 # Before creating a PR:
-pad list conventions --field trigger=on-pr-create --field status=active --format json
+pad item list conventions --field trigger=on-pr-create --field status=active --format json
 
 # Before committing:
-pad list conventions --field trigger=on-commit --field status=active --format json
+pad item list conventions --field trigger=on-commit --field status=active --format json
 
 # Before planning:
-pad list conventions --field trigger=on-plan --field status=active --format json
+pad item list conventions --field trigger=on-plan --field status=active --format json
 ```
 
 Follow ALL returned conventions. If a playbook exists for the action, follow its steps in order. Conventions are project-specific rules the team has established — they override your defaults.
@@ -119,58 +119,58 @@ Follow ALL returned conventions. If a playbook exists for the action, follow its
 ```bash
 # Create items (collection accepts singular or plural: task/tasks, idea/ideas, etc.)
 # The CLI prints the new item's issue ID (e.g. "Created TASK-5: ...") — use it for subsequent commands
-pad create <collection> "title" [--status X] [--priority X] [--assignee X] [--category X] [--content "..."] [--stdin]
-pad create task "Fix OAuth redirect" --priority high
-pad create idea "Real-time collaboration" --category infrastructure
-pad create phase "API Redesign" --status active
-pad create doc "Auth Architecture" --category architecture --stdin <<< "# Auth Architecture\n\n..."
+pad item create <collection> "title" [--status X] [--priority X] [--assignee X] [--category X] [--content "..."] [--stdin]
+pad item create task "Fix OAuth redirect" --priority high
+pad item create idea "Real-time collaboration" --category infrastructure
+pad item create phase "API Redesign" --status active
+pad item create doc "Auth Architecture" --category architecture --stdin <<< "# Auth Architecture\n\n..."
 
 # Custom fields via --field flag (works for any collection's fields)
-pad create convention "Run tests" --field trigger=on-task-complete --field scope=all --field priority=must
-pad create roadmap "Feature X" --field quarter=2026-Q3
+pad item create convention "Run tests" --field trigger=on-task-complete --field scope=all --field priority=must
+pad item create roadmap "Feature X" --field quarter=2026-Q3
 
 # List items (defaults to non-done items)
-pad list [collection] [--status X] [--priority X] [--all] [--field key=value] [--format json]
-pad list tasks                        # open + in_progress tasks
-pad list tasks --status done          # completed tasks
-pad list conventions --field trigger=always --field status=active  # filtered by custom fields
-pad list --all                        # everything across all collections
+pad item list [collection] [--status X] [--priority X] [--all] [--field key=value] [--format json]
+pad item list tasks                   # open + in_progress tasks
+pad item list tasks --status done     # completed tasks
+pad item list conventions --field trigger=always --field status=active  # filtered by custom fields
+pad item list --all                   # everything across all collections
 
 # Show item detail — use the issue ID (e.g. TASK-5, BUG-8)
-pad show TASK-5 [--format json|markdown]
+pad item show TASK-5 [--format json|markdown]
 
 # Update items — use the issue ID
-pad update TASK-5 --status done
-pad update IDEA-3 --priority high --assignee dave
-pad update DOC-1 --stdin < updated-doc.md
+pad item update TASK-5 --status done
+pad item update IDEA-3 --priority high --assignee dave
+pad item update DOC-1 --stdin < updated-doc.md
 
 # Delete (archive) — use the issue ID
-pad delete TASK-5
+pad item delete TASK-5
 
 # Search
-pad search "query" [--format json]
+pad item search "query" [--format json]
 ```
 
 ### Intelligence
 ```bash
-pad status [--format json]            # Project dashboard
-pad next [--format json]              # Recommended next task
-pad standup [--days N] [--format json]  # Daily standup report (completed/in-progress/blockers)
-pad changelog [--days N] [--since DATE] [--phase PHASE-2] [--format json|markdown]  # Release notes
+pad project dashboard [--format json]  # Project dashboard
+pad project next [--format json]       # Recommended next task
+pad project standup [--days N] [--format json]  # Daily standup report (completed/in-progress/blockers)
+pad project changelog [--days N] [--since DATE] [--phase PHASE-2] [--format json|markdown]  # Release notes
 ```
 
 ### Dependencies
 ```bash
-pad blocks TASK-5 TASK-8              # "TASK-5 blocks TASK-8"
-pad blocked-by TASK-5 TASK-3          # "TASK-5 is blocked by TASK-3"
-pad deps TASK-5                       # Show all dependencies for an item
-pad unblock TASK-5 TASK-8             # Remove a dependency
+pad item block TASK-5 TASK-8          # "TASK-5 blocks TASK-8"
+pad item blocked-by TASK-5 TASK-3     # "TASK-5 is blocked by TASK-3"
+pad item deps TASK-5                  # Show all dependencies for an item
+pad item unblock TASK-5 TASK-8        # Remove a dependency
 ```
 
 ### Collections
 ```bash
-pad collections [--format json]       # List collections with counts
-pad collections create "Name" --fields "key:type[:options]; ..." [--icon "X"]
+pad collection list [--format json]   # List collections with counts
+pad collection create "Name" --fields "key:type[:options]; ..." [--icon "X"]
 ```
 
 ### Webhooks
@@ -189,38 +189,38 @@ All commands support `--format json` (for parsing) or `--format table` (default,
 
 ### Ideation: "Let's brainstorm about X"
 
-1. **Load context:** Run `pad status --format json` and `pad list --format json --limit 20`
-2. **Search for related items:** `pad search "X" --format json`
+1. **Load context:** Run `pad project dashboard --format json` and `pad item list --format json --limit 20`
+2. **Search for related items:** `pad item search "X" --format json`
 3. **Discuss systematically:** Ask clarifying questions, explore trade-offs, reference existing items with [[Title]] links
 4. **Offer to save:** At natural checkpoints, offer to create items:
-   - "Want me to save this as an Idea?" → `pad create idea "X" --content "..." --stdin`
-   - "Should I create a Doc for this architecture decision?" → `pad create doc "X" --category decision --stdin`
+   - "Want me to save this as an Idea?" → `pad item create idea "X" --content "..." --stdin`
+   - "Should I create a Doc for this architecture decision?" → `pad item create doc "X" --category decision --stdin`
 5. **Never save without asking.** Always show what you'll create and get confirmation.
 
 ### Planning: "Let's plan the next phase"
 
-1. **Load context:** `pad status --format json`, `pad list phases --all --format json`
+1. **Load context:** `pad project dashboard --format json`, `pad item list phases --all --format json`
 2. **Understand current state:** What phases exist? What's active? What's completed?
 3. **Propose outline:** Present phase title + 1-line summary. Ask for feedback.
-4. **Create the phase:** `pad create phase "Phase N: Title" --status draft --stdin <<< "<plan content>"`
+4. **Create the phase:** `pad item create phase "Phase N: Title" --status draft --stdin <<< "<plan content>"`
 5. **Decompose into tasks:** For each task in the plan, create a Task item:
    ```bash
-   pad create task "Task description" --phase PHASE-3 --priority medium
+   pad item create task "Task description" --phase PHASE-3 --priority medium
    ```
 6. **Each task should be PR-sized** — small enough for one branch, large enough to be meaningful.
 7. **Ask before creating each item.** Don't bulk-create without approval.
 
 ### Decomposition: "Break phase X into tasks"
 
-1. **Load the phase:** `pad show PHASE-2 --format markdown`
+1. **Load the phase:** `pad item show PHASE-2 --format markdown`
 2. **Analyze the content** for actionable work items
 3. **Propose task list** with titles and priorities
-4. **Create approved tasks:** One `pad create task` per approved item
+4. **Create approved tasks:** One `pad item create task` per approved item
 5. **Link tasks to phase** using `--phase PHASE-2` flag (if the phase collection has a relation field)
 
 ### Status Check: "How are we doing?"
 
-1. Run `pad status --format json`
+1. Run `pad project dashboard --format json`
 2. Present conversationally:
    - Collection summaries (Tasks: 5 open, 2 in progress, 12 done)
    - Active phase progress with bars
@@ -230,14 +230,14 @@ All commands support `--format json` (for parsing) or `--format table` (default,
 
 ### Daily Standup: "Prep for standup"
 
-1. Run `pad list tasks --status done --format json` (recently completed)
-2. Run `pad list tasks --status in-progress --format json` (current work)
-3. Run `pad status --format json` for blockers/attention items
+1. Run `pad item list tasks --status done --format json` (recently completed)
+2. Run `pad item list tasks --status in-progress --format json` (current work)
+3. Run `pad project dashboard --format json` for blockers/attention items
 4. Present as: Yesterday / Today / Blockers format
 
 ### Onboarding: "Scan this codebase" / "Set up my workspace"
 
-1. **Check workspace state:** `pad status --format json` — if the workspace already has items, ask if they want to add more or start fresh sections.
+1. **Check workspace state:** `pad project dashboard --format json` — if the workspace already has items, ask if they want to add more or start fresh sections.
 2. **Analyze the codebase:** Read key project files to understand the project:
    - `README.md` or `README` — project overview, setup instructions
    - `CLAUDE.md` — existing AI/agent instructions
@@ -256,15 +256,15 @@ All commands support `--format json` (for parsing) or `--format table` (default,
 
 ### Retrospective: "Phase X is done, let's retro"
 
-1. Load the phase: `pad show PHASE-2 --format markdown`
-2. Load tasks: `pad list tasks --all --format json` (filter to phase)
+1. Load the phase: `pad item show PHASE-2 --format markdown`
+2. Load tasks: `pad item list tasks --all --format json` (filter to phase)
 3. Generate retro: What shipped, what was deferred, lessons learned
-4. Offer to save: `pad create doc "Phase N Retrospective" --category retro --stdin`
-5. Offer to update phase status: `pad update PHASE-2 --status completed`
+4. Offer to save: `pad item create doc "Phase N Retrospective" --category retro --stdin`
+5. Offer to update phase status: `pad item update PHASE-2 --status completed`
 
 ## Key Principles
 
-1. **Use issue IDs, not slugs.** Every item has an ID like `TASK-5` or `BUG-8`. Use these in all commands: `pad show TASK-5`, `pad update BUG-8 --status done`. The CLI prints issue IDs in all output — look for them.
+1. **Use issue IDs, not slugs.** Every item has an ID like `TASK-5` or `BUG-8`. Use these in all commands: `pad item show TASK-5`, `pad item update BUG-8 --status done`. The CLI prints issue IDs in all output — look for them.
 2. **Discuss before acting.** Always show what you plan to create/modify and get confirmation.
 3. **Use the CLI.** Every action goes through `pad` commands — don't try to modify the database directly.
 4. **Be conversational.** You're not a command executor. You're a project partner.
@@ -272,11 +272,11 @@ All commands support `--format json` (for parsing) or `--format table` (default,
 6. **Keep it practical.** Tasks should be PR-sized. Ideas should be actionable. Docs should be concise.
 7. **Attribution matters.** Items you create will have `created_by: agent` and `source: cli` automatically.
 8. **Follow project conventions.** Always load and follow active conventions before performing work. They are project-specific rules that override your defaults.
-9. **Learn and teach.** When the user corrects your behavior or teaches you a project-specific rule, offer to save it as a convention: "Should I save this as a project convention so future agents follow it too?" Use `pad create convention "Title" --field trigger=<inferred> --field scope=<inferred> --field priority=should --stdin` with an appropriate trigger inferred from the context.
+9. **Learn and teach.** When the user corrects your behavior or teaches you a project-specific rule, offer to save it as a convention: "Should I save this as a project convention so future agents follow it too?" Use `pad item create convention "Title" --field trigger=<inferred> --field scope=<inferred> --field priority=should --stdin` with an appropriate trigger inferred from the context.
 
 ## Anything Else
 
 If the user's intent doesn't match any pattern above, respond helpfully. You can always:
-- Run `pad list` or `pad search` to find relevant items
-- Run `pad show TASK-5` to load any item's detail (use the issue ID from list output)
+- Run `pad item list` or `pad item search` to find relevant items
+- Run `pad item show TASK-5` to load any item's detail (use the issue ID from list output)
 - Suggest the appropriate workflow based on what they're trying to do
diff --git a/web/src/lib/components/OnboardingChecklist.svelte b/web/src/lib/components/OnboardingChecklist.svelte
index 0b855334..75af8c01 100644
--- a/web/src/lib/components/OnboardingChecklist.svelte
+++ b/web/src/lib/components/OnboardingChecklist.svelte
@@ -127,7 +127,7 @@
 
 	<div class="onboarding-footer">
 		<p class="footer-instructions">
-			Install the Pad skill in your project with <code>pad init</code>, then paste a prompt above into Claude Code or your favorite AI agent.
+			Install the Pad skill in your project with <code>pad agent install</code>, then paste a prompt above into Claude Code or your favorite AI agent.
 		</p>
 		<a href="/{wsSlug}/library" class="footer-link">Or browse the library for conventions and playbooks</a>
 	</div>
diff --git a/web/src/lib/components/auth/SetupRequiredNotice.svelte b/web/src/lib/components/auth/SetupRequiredNotice.svelte
index 6387c9d4..e26200bb 100644
--- a/web/src/lib/components/auth/SetupRequiredNotice.svelte
+++ b/web/src/lib/components/auth/SetupRequiredNotice.svelte
@@ -25,16 +25,16 @@
 		<div class="instructions">
 			<div class="instruction">
 				<p class="instruction-label">Local server</p>
-				<code>pad setup</code>
+				<code>pad auth setup</code>
 			</div>
 
 			<div class="instruction">
 				<p class="instruction-label">Docker</p>
-				<code>docker exec -it &lt;container&gt; pad setup</code>
+				<code>docker exec -it &lt;container&gt; pad auth setup</code>
 			</div>
 		</div>
 
-		<p class="hint">If this Pad server runs on another machine, run <code>pad setup</code> there instead.</p>
+		<p class="hint">If this Pad server runs on another machine, run <code>pad auth setup</code> there instead.</p>
 	{/if}
 
 	{#if nextStep}
diff --git a/web/src/routes/+page.svelte b/web/src/routes/+page.svelte
index fe8b9266..28c89931 100644
--- a/web/src/routes/+page.svelte
+++ b/web/src/routes/+page.svelte
@@ -22,7 +22,7 @@
 	{:else if workspaceStore.workspaces.length === 0}
 		<h1>Welcome to Pad</h1>
 		<p>Create a workspace to get started.</p>
-		<p class="hint">Run <code>pad init</code> in your project directory, or use the workspace switcher in the sidebar.</p>
+		<p class="hint">Run <code>pad workspace init</code> in your project directory, or use the workspace switcher in the sidebar.</p>
 	{:else}
 		<p>Redirecting...</p>
 	{/if}