3 files changed, 682 insertions, 679 deletions

diff --git a/cmd/ship/deploy.go b/cmd/ship/deploy.go
new file mode 100644
index 0000000..24eed1e
--- /dev/null
+++ b/cmd/ship/deploy.go
@@ -0,0 +1,598 @@
+package main
+
+import (
+        "bufio"
+        "fmt"
+        "os"
+        "path/filepath"
+        "strconv"
+        "strings"
+
+        "github.com/bdw/ship/internal/ssh"
+        "github.com/bdw/ship/internal/state"
+        "github.com/bdw/ship/internal/templates"
+        "github.com/spf13/cobra"
+)
+
+// DeployOptions contains all options for deploying or updating an app
+type DeployOptions struct {
+        Host     string
+        Domain   string
+        Name     string
+        Binary   string
+        Dir      string // for static sites
+        Port     int
+        Args     string
+        Files    []string
+        Memory   string
+        CPU      string
+        Env      map[string]string // merged env vars
+        IsUpdate bool
+}
+
+func runDeploy(cmd *cobra.Command, args []string) error {
+        flags := cmd.Flags()
+
+        // Parse CLI flags
+        binary, _ := flags.GetString("binary")
+        static, _ := flags.GetBool("static")
+        dir, _ := flags.GetString("dir")
+        domain, _ := flags.GetString("domain")
+        name, _ := flags.GetString("name")
+        port, _ := flags.GetInt("port")
+        envVars, _ := flags.GetStringArray("env")
+        envFile, _ := flags.GetString("env-file")
+        argsFlag, _ := flags.GetString("args")
+        files, _ := flags.GetStringArray("file")
+        memory, _ := flags.GetString("memory")
+        cpu, _ := flags.GetString("cpu")
+
+        // Get host from flag or state default
+        host := hostFlag
+        if host == "" {
+                st, err := state.Load()
+                if err != nil {
+                        return fmt.Errorf("error loading state: %w", err)
+                }
+                host = st.GetDefaultHost()
+        }
+
+        // If no flags provided, show help
+        if domain == "" && binary == "" && !static && name == "" {
+                return cmd.Help()
+        }
+
+        if host == "" {
+                return fmt.Errorf("--host is required")
+        }
+
+        // Load state once - this will be used throughout
+        st, err := state.Load()
+        if err != nil {
+                return fmt.Errorf("error loading state: %w", err)
+        }
+        hostState := st.GetHost(host)
+
+        // Config update mode: --name provided without --binary or --static
+        if name != "" && binary == "" && !static {
+                existingApp, err := st.GetApp(host, name)
+                if err != nil {
+                        return fmt.Errorf("app %s not found (use --binary to deploy a new app)", name)
+                }
+
+                // Build merged config starting from existing app
+                opts := DeployOptions{
+                        Host:   host,
+                        Name:   name,
+                        Port:   existingApp.Port,
+                        Args:   existingApp.Args,
+                        Files:  existingApp.Files,
+                        Memory: existingApp.Memory,
+                        CPU:    existingApp.CPU,
+                        Env:    make(map[string]string),
+                }
+                for k, v := range existingApp.Env {
+                        opts.Env[k] = v
+                }
+
+                // Override with CLI flags if provided
+                if argsFlag != "" {
+                        opts.Args = argsFlag
+                }
+                if len(files) > 0 {
+                        opts.Files = files
+                }
+                if memory != "" {
+                        opts.Memory = memory
+                }
+                if cpu != "" {
+                        opts.CPU = cpu
+                }
+
+                // Merge env vars (CLI overrides existing)
+                for _, e := range envVars {
+                        parts := strings.SplitN(e, "=", 2)
+                        if len(parts) == 2 {
+                                opts.Env[parts[0]] = parts[1]
+                        }
+                }
+                if envFile != "" {
+                        fileEnv, err := parseEnvFile(envFile)
+                        if err != nil {
+                                return fmt.Errorf("error reading env file: %w", err)
+                        }
+                        for k, v := range fileEnv {
+                                opts.Env[k] = v
+                        }
+                }
+
+                return updateAppConfig(st, opts)
+        }
+
+        // Infer name early so we can use it for subdomain generation and existing app lookup
+        if name == "" {
+                if static {
+                        name = domain
+                        if name == "" && hostState.BaseDomain != "" {
+                                name = filepath.Base(dir)
+                        }
+                } else {
+                        name = filepath.Base(binary)
+                }
+        }
+
+        // Check if this is an update to an existing app/site
+        existingApp, _ := st.GetApp(host, name)
+        isUpdate := existingApp != nil
+
+        // For new deployments, require domain or base domain
+        if !isUpdate && domain == "" && hostState.BaseDomain == "" {
+                return fmt.Errorf("--domain required (or configure base domain with 'ship host init --base-domain')")
+        }
+
+        // Build merged config, starting from existing app if updating
+        opts := DeployOptions{
+                Host:     host,
+                Name:     name,
+                Binary:   binary,
+                Dir:      dir,
+                IsUpdate: isUpdate,
+        }
+
+        // Merge domain: auto-subdomain + (user-provided or existing custom domain)
+        var domains []string
+        if hostState.BaseDomain != "" {
+                domains = append(domains, name+"."+hostState.BaseDomain)
+        }
+        if domain != "" {
+                domains = append(domains, domain)
+        } else if isUpdate && existingApp.Domain != "" {
+                for _, d := range strings.Split(existingApp.Domain, ",") {
+                        d = strings.TrimSpace(d)
+                        if d != "" && (hostState.BaseDomain == "" || !strings.HasSuffix(d, "."+hostState.BaseDomain)) {
+                                domains = append(domains, d)
+                        }
+                }
+        }
+        opts.Domain = strings.Join(domains, ", ")
+
+        // For apps, merge all config fields
+        if !static {
+                // Start with existing values if updating
+                if isUpdate {
+                        opts.Port = existingApp.Port
+                        opts.Args = existingApp.Args
+                        opts.Files = existingApp.Files
+                        opts.Memory = existingApp.Memory
+                        opts.CPU = existingApp.CPU
+                        opts.Env = make(map[string]string)
+                        for k, v := range existingApp.Env {
+                                opts.Env[k] = v
+                        }
+                } else {
+                        opts.Port = port
+                        opts.Env = make(map[string]string)
+                }
+
+                // Override with CLI flags if provided
+                if argsFlag != "" {
+                        opts.Args = argsFlag
+                }
+                if len(files) > 0 {
+                        opts.Files = files
+                }
+                if memory != "" {
+                        opts.Memory = memory
+                }
+                if cpu != "" {
+                        opts.CPU = cpu
+                }
+
+                // Merge env vars (CLI overrides existing)
+                for _, e := range envVars {
+                        parts := strings.SplitN(e, "=", 2)
+                        if len(parts) == 2 {
+                                opts.Env[parts[0]] = parts[1]
+                        }
+                }
+                if envFile != "" {
+                        fileEnv, err := parseEnvFile(envFile)
+                        if err != nil {
+                                return fmt.Errorf("error reading env file: %w", err)
+                        }
+                        for k, v := range fileEnv {
+                                opts.Env[k] = v
+                        }
+                }
+        }
+
+        if static {
+                return deployStatic(st, opts)
+        }
+        return deployApp(st, opts)
+}
+
+func deployApp(st *state.State, opts DeployOptions) error {
+        if opts.Binary == "" {
+                return fmt.Errorf("--binary is required")
+        }
+
+        if _, err := os.Stat(opts.Binary); err != nil {
+                return fmt.Errorf("binary not found: %s", opts.Binary)
+        }
+
+        fmt.Printf("Deploying app: %s\n", opts.Name)
+        fmt.Printf("  Domain(s): %s\n", opts.Domain)
+        fmt.Printf("  Binary: %s\n", opts.Binary)
+
+        // Allocate port for new apps
+        port := opts.Port
+        if opts.IsUpdate {
+                fmt.Printf("  Updating existing deployment (port %d)\n", port)
+        } else {
+                if port == 0 {
+                        port = st.AllocatePort(opts.Host)
+                }
+                fmt.Printf("  Allocated port: %d\n", port)
+        }
+
+        // Add PORT to env
+        opts.Env["PORT"] = strconv.Itoa(port)
+
+        client, err := ssh.Connect(opts.Host)
+        if err != nil {
+                return fmt.Errorf("error connecting to VPS: %w", err)
+        }
+        defer client.Close()
+
+        fmt.Println("-> Uploading binary...")
+        remoteTmpPath := fmt.Sprintf("/tmp/%s", opts.Name)
+        if err := client.Upload(opts.Binary, remoteTmpPath); err != nil {
+                return fmt.Errorf("error uploading binary: %w", err)
+        }
+
+        fmt.Println("-> Creating system user...")
+        client.RunSudo(fmt.Sprintf("useradd -r -s /bin/false %s", opts.Name))
+
+        fmt.Println("-> Setting up directories...")
+        workDir := fmt.Sprintf("/var/lib/%s", opts.Name)
+        if _, err := client.RunSudo(fmt.Sprintf("mkdir -p %s", workDir)); err != nil {
+                return fmt.Errorf("error creating work directory: %w", err)
+        }
+        if _, err := client.RunSudo(fmt.Sprintf("chown %s:%s %s", opts.Name, opts.Name, workDir)); err != nil {
+                return fmt.Errorf("error setting work directory ownership: %w", err)
+        }
+
+        fmt.Println("-> Installing binary...")
+        binaryDest := fmt.Sprintf("/usr/local/bin/%s", opts.Name)
+        if _, err := client.RunSudo(fmt.Sprintf("mv %s %s", remoteTmpPath, binaryDest)); err != nil {
+                return fmt.Errorf("error moving binary: %w", err)
+        }
+        if _, err := client.RunSudo(fmt.Sprintf("chmod +x %s", binaryDest)); err != nil {
+                return fmt.Errorf("error making binary executable: %w", err)
+        }
+
+        if len(opts.Files) > 0 {
+                fmt.Println("-> Uploading config files...")
+                for _, file := range opts.Files {
+                        if _, err := os.Stat(file); err != nil {
+                                return fmt.Errorf("config file not found: %s", file)
+                        }
+
+                        remotePath := fmt.Sprintf("%s/%s", workDir, filepath.Base(file))
+                        fileTmpPath := fmt.Sprintf("/tmp/%s_%s", opts.Name, filepath.Base(file))
+
+                        if err := client.Upload(file, fileTmpPath); err != nil {
+                                return fmt.Errorf("error uploading config file %s: %w", file, err)
+                        }
+
+                        if _, err := client.RunSudo(fmt.Sprintf("mv %s %s", fileTmpPath, remotePath)); err != nil {
+                                return fmt.Errorf("error moving config file %s: %w", file, err)
+                        }
+
+                        if _, err := client.RunSudo(fmt.Sprintf("chown %s:%s %s", opts.Name, opts.Name, remotePath)); err != nil {
+                                return fmt.Errorf("error setting config file ownership %s: %w", file, err)
+                        }
+
+                        fmt.Printf("  Uploaded: %s\n", file)
+                }
+        }
+
+        fmt.Println("-> Creating environment file...")
+        envFilePath := fmt.Sprintf("/etc/ship/env/%s.env", opts.Name)
+        envContent := ""
+        for k, v := range opts.Env {
+                envContent += fmt.Sprintf("%s=%s\n", k, v)
+        }
+        if err := client.WriteSudoFile(envFilePath, envContent); err != nil {
+                return fmt.Errorf("error creating env file: %w", err)
+        }
+        if _, err := client.RunSudo(fmt.Sprintf("chmod 600 %s", envFilePath)); err != nil {
+                return fmt.Errorf("error setting env file permissions: %w", err)
+        }
+        if _, err := client.RunSudo(fmt.Sprintf("chown %s:%s %s", opts.Name, opts.Name, envFilePath)); err != nil {
+                return fmt.Errorf("error setting env file ownership: %w", err)
+        }
+
+        fmt.Println("-> Creating systemd service...")
+        serviceContent, err := templates.SystemdService(map[string]string{
+                "Name":       opts.Name,
+                "User":       opts.Name,
+                "WorkDir":    workDir,
+                "BinaryPath": binaryDest,
+                "Port":       strconv.Itoa(port),
+                "EnvFile":    envFilePath,
+                "Args":       opts.Args,
+                "Memory":     opts.Memory,
+                "CPU":        opts.CPU,
+        })
+        if err != nil {
+                return fmt.Errorf("error generating systemd unit: %w", err)
+        }
+
+        servicePath := fmt.Sprintf("/etc/systemd/system/%s.service", opts.Name)
+        if err := client.WriteSudoFile(servicePath, serviceContent); err != nil {
+                return fmt.Errorf("error creating systemd unit: %w", err)
+        }
+
+        fmt.Println("-> Configuring Caddy...")
+        caddyContent, err := templates.AppCaddy(map[string]string{
+                "Domain": opts.Domain,
+                "Port":   strconv.Itoa(port),
+        })
+        if err != nil {
+                return fmt.Errorf("error generating Caddy config: %w", err)
+        }
+
+        caddyPath := fmt.Sprintf("/etc/caddy/sites-enabled/%s.caddy", opts.Name)
+        if err := client.WriteSudoFile(caddyPath, caddyContent); err != nil {
+                return fmt.Errorf("error creating Caddy config: %w", err)
+        }
+
+        fmt.Println("-> Reloading systemd...")
+        if _, err := client.RunSudo("systemctl daemon-reload"); err != nil {
+                return fmt.Errorf("error reloading systemd: %w", err)
+        }
+
+        fmt.Println("-> Starting service...")
+        if _, err := client.RunSudo(fmt.Sprintf("systemctl enable %s", opts.Name)); err != nil {
+                return fmt.Errorf("error enabling service: %w", err)
+        }
+        if _, err := client.RunSudo(fmt.Sprintf("systemctl restart %s", opts.Name)); err != nil {
+                return fmt.Errorf("error starting service: %w", err)
+        }
+
+        fmt.Println("-> Reloading Caddy...")
+        if _, err := client.RunSudo("systemctl reload caddy"); err != nil {
+                return fmt.Errorf("error reloading Caddy: %w", err)
+        }
+
+        st.AddApp(opts.Host, opts.Name, &state.App{
+                Type:   "app",
+                Domain: opts.Domain,
+                Port:   port,
+                Env:    opts.Env,
+                Args:   opts.Args,
+                Files:  opts.Files,
+                Memory: opts.Memory,
+                CPU:    opts.CPU,
+        })
+        if err := st.Save(); err != nil {
+                return fmt.Errorf("error saving state: %w", err)
+        }
+
+        fmt.Printf("\n App deployed successfully!\n")
+        // Show first domain in the URL message
+        primaryDomain := strings.Split(opts.Domain, ",")[0]
+        primaryDomain = strings.TrimSpace(primaryDomain)
+        fmt.Printf("  https://%s (may take a minute for HTTPS cert)\n", primaryDomain)
+        return nil
+}
+
+func updateAppConfig(st *state.State, opts DeployOptions) error {
+        existingApp, err := st.GetApp(opts.Host, opts.Name)
+        if err != nil {
+                return fmt.Errorf("app %s not found (use --binary to deploy a new app)", opts.Name)
+        }
+
+        if existingApp.Type != "app" {
+                return fmt.Errorf("%s is a static site, not an app", opts.Name)
+        }
+
+        fmt.Printf("Updating config: %s\n", opts.Name)
+
+        // Add PORT to env
+        opts.Env["PORT"] = strconv.Itoa(existingApp.Port)
+
+        client, err := ssh.Connect(opts.Host)
+        if err != nil {
+                return fmt.Errorf("error connecting to VPS: %w", err)
+        }
+        defer client.Close()
+
+        // Update env file
+        fmt.Println("-> Updating environment file...")
+        envFilePath := fmt.Sprintf("/etc/ship/env/%s.env", opts.Name)
+        envContent := ""
+        for k, v := range opts.Env {
+                envContent += fmt.Sprintf("%s=%s\n", k, v)
+        }
+        if err := client.WriteSudoFile(envFilePath, envContent); err != nil {
+                return fmt.Errorf("error creating env file: %w", err)
+        }
+
+        // Regenerate systemd unit
+        fmt.Println("-> Updating systemd service...")
+        workDir := fmt.Sprintf("/var/lib/%s", opts.Name)
+        binaryDest := fmt.Sprintf("/usr/local/bin/%s", opts.Name)
+        serviceContent, err := templates.SystemdService(map[string]string{
+                "Name":       opts.Name,
+                "User":       opts.Name,
+                "WorkDir":    workDir,
+                "BinaryPath": binaryDest,
+                "Port":       strconv.Itoa(existingApp.Port),
+                "EnvFile":    envFilePath,
+                "Args":       opts.Args,
+                "Memory":     opts.Memory,
+                "CPU":        opts.CPU,
+        })
+        if err != nil {
+                return fmt.Errorf("error generating systemd unit: %w", err)
+        }
+
+        servicePath := fmt.Sprintf("/etc/systemd/system/%s.service", opts.Name)
+        if err := client.WriteSudoFile(servicePath, serviceContent); err != nil {
+                return fmt.Errorf("error creating systemd unit: %w", err)
+        }
+
+        fmt.Println("-> Reloading systemd...")
+        if _, err := client.RunSudo("systemctl daemon-reload"); err != nil {
+                return fmt.Errorf("error reloading systemd: %w", err)
+        }
+
+        fmt.Println("-> Restarting service...")
+        if _, err := client.RunSudo(fmt.Sprintf("systemctl restart %s", opts.Name)); err != nil {
+                return fmt.Errorf("error restarting service: %w", err)
+        }
+
+        // Update state
+        existingApp.Args = opts.Args
+        existingApp.Memory = opts.Memory
+        existingApp.CPU = opts.CPU
+        existingApp.Env = opts.Env
+        if err := st.Save(); err != nil {
+                return fmt.Errorf("error saving state: %w", err)
+        }
+
+        fmt.Printf("\n Config updated successfully!\n")
+        return nil
+}
+
+func deployStatic(st *state.State, opts DeployOptions) error {
+        if _, err := os.Stat(opts.Dir); err != nil {
+                return fmt.Errorf("directory not found: %s", opts.Dir)
+        }
+
+        fmt.Printf("Deploying static site: %s\n", opts.Name)
+        fmt.Printf("  Domain(s): %s\n", opts.Domain)
+        fmt.Printf("  Directory: %s\n", opts.Dir)
+
+        if opts.IsUpdate {
+                fmt.Println("  Updating existing deployment")
+        }
+
+        client, err := ssh.Connect(opts.Host)
+        if err != nil {
+                return fmt.Errorf("error connecting to VPS: %w", err)
+        }
+        defer client.Close()
+
+        remoteDir := fmt.Sprintf("/var/www/%s", opts.Name)
+        fmt.Println("-> Creating remote directory...")
+        if _, err := client.RunSudo(fmt.Sprintf("mkdir -p %s", remoteDir)); err != nil {
+                return fmt.Errorf("error creating remote directory: %w", err)
+        }
+
+        currentUser, err := client.Run("whoami")
+        if err != nil {
+                return fmt.Errorf("error getting current user: %w", err)
+        }
+        currentUser = strings.TrimSpace(currentUser)
+
+        if _, err := client.RunSudo(fmt.Sprintf("chown -R %s:%s %s", currentUser, currentUser, remoteDir)); err != nil {
+                return fmt.Errorf("error setting temporary ownership: %w", err)
+        }
+
+        fmt.Println("-> Uploading files...")
+        if err := client.UploadDir(opts.Dir, remoteDir); err != nil {
+                return fmt.Errorf("error uploading files: %w", err)
+        }
+
+        fmt.Println("-> Setting permissions...")
+        if _, err := client.RunSudo(fmt.Sprintf("chown -R www-data:www-data %s", remoteDir)); err != nil {
+                return fmt.Errorf("error setting ownership: %w", err)
+        }
+        if _, err := client.RunSudo(fmt.Sprintf("chmod -R 755 %s", remoteDir)); err != nil {
+                return fmt.Errorf("error setting directory permissions: %w", err)
+        }
+        if _, err := client.RunSudo(fmt.Sprintf("find %s -type f -exec chmod 644 {} \\;", remoteDir)); err != nil {
+                return fmt.Errorf("error setting file permissions: %w", err)
+        }
+
+        fmt.Println("-> Configuring Caddy...")
+        caddyContent, err := templates.StaticCaddy(map[string]string{
+                "Domain":  opts.Domain,
+                "RootDir": remoteDir,
+        })
+        if err != nil {
+                return fmt.Errorf("error generating Caddy config: %w", err)
+        }
+
+        caddyPath := fmt.Sprintf("/etc/caddy/sites-enabled/%s.caddy", opts.Name)
+        if err := client.WriteSudoFile(caddyPath, caddyContent); err != nil {
+                return fmt.Errorf("error creating Caddy config: %w", err)
+        }
+
+        fmt.Println("-> Reloading Caddy...")
+        if _, err := client.RunSudo("systemctl reload caddy"); err != nil {
+                return fmt.Errorf("error reloading Caddy: %w", err)
+        }
+
+        st.AddApp(opts.Host, opts.Name, &state.App{
+                Type:   "static",
+                Domain: opts.Domain,
+        })
+        if err := st.Save(); err != nil {
+                return fmt.Errorf("error saving state: %w", err)
+        }
+
+        fmt.Printf("\n Static site deployed successfully!\n")
+        primaryDomain := strings.Split(opts.Domain, ",")[0]
+        primaryDomain = strings.TrimSpace(primaryDomain)
+        fmt.Printf("  https://%s (may take a minute for HTTPS cert)\n", primaryDomain)
+        return nil
+}
+
+func parseEnvFile(path string) (map[string]string, error) {
+        file, err := os.Open(path)
+        if err != nil {
+                return nil, err
+        }
+        defer file.Close()
+
+        env := make(map[string]string)
+        scanner := bufio.NewScanner(file)
+        for scanner.Scan() {
+                line := strings.TrimSpace(scanner.Text())
+                if line == "" || strings.HasPrefix(line, "#") {
+                        continue
+                }
+
+                parts := strings.SplitN(line, "=", 2)
+                if len(parts) == 2 {
+                        env[parts[0]] = parts[1]
+                }
+        }
+
+        return env, scanner.Err()
+}
diff --git a/cmd/ship/main.go b/cmd/ship/main.go
index cd2b0c1..f7d95c1 100644
--- a/cmd/ship/main.go
+++ b/cmd/ship/main.go
@@ -3,100 +3,8 @@ package main
 import (
         "fmt"
         "os"
-
-        "github.com/bdw/ship/cmd/ship/env"
-        "github.com/bdw/ship/cmd/ship/host"
-        "github.com/spf13/cobra"
 )
 
-var (
-        // Persistent flags
-        hostFlag string
-
-        // Version info (set via ldflags)
-        version = "dev"
-        commit  = "none"
-        date    = "unknown"
-)
-
-const banner = `
-        ~
-    ___|___
-   |   _   |
-  _|__|_|__|_
- |   SHIP   |  Ship apps to your VPS
-  \_________/   with automatic HTTPS
-   ~~~~~~~~~
-`
-
-var rootCmd = &cobra.Command{
-        Use:   "ship",
-        Short: "Ship apps and static sites to a VPS with automatic HTTPS",
-        Long: banner + `
-A CLI tool for deploying applications and static sites to a VPS.
-
-How it works:
-  Ship uses only SSH to deploy - no agents, containers, or external services.
-  It uploads your binary or static website, creates a systemd service, and configures Caddy
-  for automatic HTTPS. Ports are assigned automatically. Your app runs directly on the VPS
-  with minimal overhead.
-
-Requirements:
-  • A VPS with SSH access (use 'ship host init' to set up a new server)
-  • An SSH config entry or user@host for your server
-  • A domain pointing to your VPS
-
-Examples:
-  # Deploy a Go binary
-  ship --binary ./myapp --domain api.example.com
-
-  # Deploy with auto-generated subdomain (requires base domain)
-  ship --binary ./myapp --name myapp
-
-  # Deploy a static site
-  ship --static --dir ./dist --domain example.com
-
-  # Update config without redeploying binary
-  ship --name myapp --memory 512M --cpu 50%
-  ship --name myapp --env DEBUG=true
-
-  # Set up a new VPS with base domain
-  ship host init --host user@vps --base-domain apps.example.com`,
-        RunE:          runDeploy,
-        SilenceUsage:  true,
-        SilenceErrors: true,
-}
-
-func init() {
-        // Persistent flags available to all subcommands
-        rootCmd.PersistentFlags().StringVar(&hostFlag, "host", "", "VPS host (SSH config alias or user@host)")
-
-        // Root command (deploy) flags
-        rootCmd.Flags().String("binary", "", "Path to Go binary (for app deployment)")
-        rootCmd.Flags().Bool("static", false, "Deploy as static site")
-        rootCmd.Flags().String("dir", ".", "Directory to deploy (for static sites)")
-        rootCmd.Flags().String("domain", "", "Custom domain (optional if base domain configured)")
-        rootCmd.Flags().String("name", "", "App name (default: inferred from binary or directory)")
-        rootCmd.Flags().Int("port", 0, "Port override (default: auto-allocate)")
-        rootCmd.Flags().StringArray("env", nil, "Environment variable (KEY=VALUE, can be specified multiple times)")
-        rootCmd.Flags().String("env-file", "", "Path to .env file")
-        rootCmd.Flags().String("args", "", "Arguments to pass to binary")
-        rootCmd.Flags().StringArray("file", nil, "Config file to upload to working directory (can be specified multiple times)")
-        rootCmd.Flags().String("memory", "", "Memory limit (e.g., 512M, 1G)")
-        rootCmd.Flags().String("cpu", "", "CPU limit (e.g., 50%, 200% for 2 cores)")
-
-        // Add subcommands
-        rootCmd.AddCommand(listCmd)
-        rootCmd.AddCommand(logsCmd)
-        rootCmd.AddCommand(statusCmd)
-        rootCmd.AddCommand(restartCmd)
-        rootCmd.AddCommand(removeCmd)
-        rootCmd.AddCommand(env.Cmd)
-        rootCmd.AddCommand(host.Cmd)
-        rootCmd.AddCommand(uiCmd)
-        rootCmd.AddCommand(versionCmd)
-}
-
 func main() {
         if err := rootCmd.Execute(); err != nil {
                 fmt.Fprintf(os.Stderr, "Error: %v\n", err)
diff --git a/cmd/ship/root.go b/cmd/ship/root.go
index 24eed1e..837fd4c 100644
--- a/cmd/ship/root.go
+++ b/cmd/ship/root.go
@@ -1,598 +1,95 @@
 package main
 
 import (
-        "bufio"
-        "fmt"
-        "os"
-        "path/filepath"
-        "strconv"
-        "strings"
-
-        "github.com/bdw/ship/internal/ssh"
-        "github.com/bdw/ship/internal/state"
-        "github.com/bdw/ship/internal/templates"
+        "github.com/bdw/ship/cmd/ship/env"
+        "github.com/bdw/ship/cmd/ship/host"
         "github.com/spf13/cobra"
 )
 
-// DeployOptions contains all options for deploying or updating an app
-type DeployOptions struct {
-        Host     string
-        Domain   string
-        Name     string
-        Binary   string
-        Dir      string // for static sites
-        Port     int
-        Args     string
-        Files    []string
-        Memory   string
-        CPU      string
-        Env      map[string]string // merged env vars
-        IsUpdate bool
-}
-
-func runDeploy(cmd *cobra.Command, args []string) error {
-        flags := cmd.Flags()
-
-        // Parse CLI flags
-        binary, _ := flags.GetString("binary")
-        static, _ := flags.GetBool("static")
-        dir, _ := flags.GetString("dir")
-        domain, _ := flags.GetString("domain")
-        name, _ := flags.GetString("name")
-        port, _ := flags.GetInt("port")
-        envVars, _ := flags.GetStringArray("env")
-        envFile, _ := flags.GetString("env-file")
-        argsFlag, _ := flags.GetString("args")
-        files, _ := flags.GetStringArray("file")
-        memory, _ := flags.GetString("memory")
-        cpu, _ := flags.GetString("cpu")
-
-        // Get host from flag or state default
-        host := hostFlag
-        if host == "" {
-                st, err := state.Load()
-                if err != nil {
-                        return fmt.Errorf("error loading state: %w", err)
-                }
-                host = st.GetDefaultHost()
-        }
-
-        // If no flags provided, show help
-        if domain == "" && binary == "" && !static && name == "" {
-                return cmd.Help()
-        }
-
-        if host == "" {
-                return fmt.Errorf("--host is required")
-        }
-
-        // Load state once - this will be used throughout
-        st, err := state.Load()
-        if err != nil {
-                return fmt.Errorf("error loading state: %w", err)
-        }
-        hostState := st.GetHost(host)
-
-        // Config update mode: --name provided without --binary or --static
-        if name != "" && binary == "" && !static {
-                existingApp, err := st.GetApp(host, name)
-                if err != nil {
-                        return fmt.Errorf("app %s not found (use --binary to deploy a new app)", name)
-                }
-
-                // Build merged config starting from existing app
-                opts := DeployOptions{
-                        Host:   host,
-                        Name:   name,
-                        Port:   existingApp.Port,
-                        Args:   existingApp.Args,
-                        Files:  existingApp.Files,
-                        Memory: existingApp.Memory,
-                        CPU:    existingApp.CPU,
-                        Env:    make(map[string]string),
-                }
-                for k, v := range existingApp.Env {
-                        opts.Env[k] = v
-                }
-
-                // Override with CLI flags if provided
-                if argsFlag != "" {
-                        opts.Args = argsFlag
-                }
-                if len(files) > 0 {
-                        opts.Files = files
-                }
-                if memory != "" {
-                        opts.Memory = memory
-                }
-                if cpu != "" {
-                        opts.CPU = cpu
-                }
-
-                // Merge env vars (CLI overrides existing)
-                for _, e := range envVars {
-                        parts := strings.SplitN(e, "=", 2)
-                        if len(parts) == 2 {
-                                opts.Env[parts[0]] = parts[1]
-                        }
-                }
-                if envFile != "" {
-                        fileEnv, err := parseEnvFile(envFile)
-                        if err != nil {
-                                return fmt.Errorf("error reading env file: %w", err)
-                        }
-                        for k, v := range fileEnv {
-                                opts.Env[k] = v
-                        }
-                }
-
-                return updateAppConfig(st, opts)
-        }
-
-        // Infer name early so we can use it for subdomain generation and existing app lookup
-        if name == "" {
-                if static {
-                        name = domain
-                        if name == "" && hostState.BaseDomain != "" {
-                                name = filepath.Base(dir)
-                        }
-                } else {
-                        name = filepath.Base(binary)
-                }
-        }
-
-        // Check if this is an update to an existing app/site
-        existingApp, _ := st.GetApp(host, name)
-        isUpdate := existingApp != nil
-
-        // For new deployments, require domain or base domain
-        if !isUpdate && domain == "" && hostState.BaseDomain == "" {
-                return fmt.Errorf("--domain required (or configure base domain with 'ship host init --base-domain')")
-        }
-
-        // Build merged config, starting from existing app if updating
-        opts := DeployOptions{
-                Host:     host,
-                Name:     name,
-                Binary:   binary,
-                Dir:      dir,
-                IsUpdate: isUpdate,
-        }
-
-        // Merge domain: auto-subdomain + (user-provided or existing custom domain)
-        var domains []string
-        if hostState.BaseDomain != "" {
-                domains = append(domains, name+"."+hostState.BaseDomain)
-        }
-        if domain != "" {
-                domains = append(domains, domain)
-        } else if isUpdate && existingApp.Domain != "" {
-                for _, d := range strings.Split(existingApp.Domain, ",") {
-                        d = strings.TrimSpace(d)
-                        if d != "" && (hostState.BaseDomain == "" || !strings.HasSuffix(d, "."+hostState.BaseDomain)) {
-                                domains = append(domains, d)
-                        }
-                }
-        }
-        opts.Domain = strings.Join(domains, ", ")
-
-        // For apps, merge all config fields
-        if !static {
-                // Start with existing values if updating
-                if isUpdate {
-                        opts.Port = existingApp.Port
-                        opts.Args = existingApp.Args
-                        opts.Files = existingApp.Files
-                        opts.Memory = existingApp.Memory
-                        opts.CPU = existingApp.CPU
-                        opts.Env = make(map[string]string)
-                        for k, v := range existingApp.Env {
-                                opts.Env[k] = v
-                        }
-                } else {
-                        opts.Port = port
-                        opts.Env = make(map[string]string)
-                }
-
-                // Override with CLI flags if provided
-                if argsFlag != "" {
-                        opts.Args = argsFlag
-                }
-                if len(files) > 0 {
-                        opts.Files = files
-                }
-                if memory != "" {
-                        opts.Memory = memory
-                }
-                if cpu != "" {
-                        opts.CPU = cpu
-                }
-
-                // Merge env vars (CLI overrides existing)
-                for _, e := range envVars {
-                        parts := strings.SplitN(e, "=", 2)
-                        if len(parts) == 2 {
-                                opts.Env[parts[0]] = parts[1]
-                        }
-                }
-                if envFile != "" {
-                        fileEnv, err := parseEnvFile(envFile)
-                        if err != nil {
-                                return fmt.Errorf("error reading env file: %w", err)
-                        }
-                        for k, v := range fileEnv {
-                                opts.Env[k] = v
-                        }
-                }
-        }
-
-        if static {
-                return deployStatic(st, opts)
-        }
-        return deployApp(st, opts)
-}
-
-func deployApp(st *state.State, opts DeployOptions) error {
-        if opts.Binary == "" {
-                return fmt.Errorf("--binary is required")
-        }
-
-        if _, err := os.Stat(opts.Binary); err != nil {
-                return fmt.Errorf("binary not found: %s", opts.Binary)
-        }
-
-        fmt.Printf("Deploying app: %s\n", opts.Name)
-        fmt.Printf("  Domain(s): %s\n", opts.Domain)
-        fmt.Printf("  Binary: %s\n", opts.Binary)
-
-        // Allocate port for new apps
-        port := opts.Port
-        if opts.IsUpdate {
-                fmt.Printf("  Updating existing deployment (port %d)\n", port)
-        } else {
-                if port == 0 {
-                        port = st.AllocatePort(opts.Host)
-                }
-                fmt.Printf("  Allocated port: %d\n", port)
-        }
-
-        // Add PORT to env
-        opts.Env["PORT"] = strconv.Itoa(port)
-
-        client, err := ssh.Connect(opts.Host)
-        if err != nil {
-                return fmt.Errorf("error connecting to VPS: %w", err)
-        }
-        defer client.Close()
-
-        fmt.Println("-> Uploading binary...")
-        remoteTmpPath := fmt.Sprintf("/tmp/%s", opts.Name)
-        if err := client.Upload(opts.Binary, remoteTmpPath); err != nil {
-                return fmt.Errorf("error uploading binary: %w", err)
-        }
-
-        fmt.Println("-> Creating system user...")
-        client.RunSudo(fmt.Sprintf("useradd -r -s /bin/false %s", opts.Name))
-
-        fmt.Println("-> Setting up directories...")
-        workDir := fmt.Sprintf("/var/lib/%s", opts.Name)
-        if _, err := client.RunSudo(fmt.Sprintf("mkdir -p %s", workDir)); err != nil {
-                return fmt.Errorf("error creating work directory: %w", err)
-        }
-        if _, err := client.RunSudo(fmt.Sprintf("chown %s:%s %s", opts.Name, opts.Name, workDir)); err != nil {
-                return fmt.Errorf("error setting work directory ownership: %w", err)
-        }
-
-        fmt.Println("-> Installing binary...")
-        binaryDest := fmt.Sprintf("/usr/local/bin/%s", opts.Name)
-        if _, err := client.RunSudo(fmt.Sprintf("mv %s %s", remoteTmpPath, binaryDest)); err != nil {
-                return fmt.Errorf("error moving binary: %w", err)
-        }
-        if _, err := client.RunSudo(fmt.Sprintf("chmod +x %s", binaryDest)); err != nil {
-                return fmt.Errorf("error making binary executable: %w", err)
-        }
-
-        if len(opts.Files) > 0 {
-                fmt.Println("-> Uploading config files...")
-                for _, file := range opts.Files {
-                        if _, err := os.Stat(file); err != nil {
-                                return fmt.Errorf("config file not found: %s", file)
-                        }
-
-                        remotePath := fmt.Sprintf("%s/%s", workDir, filepath.Base(file))
-                        fileTmpPath := fmt.Sprintf("/tmp/%s_%s", opts.Name, filepath.Base(file))
-
-                        if err := client.Upload(file, fileTmpPath); err != nil {
-                                return fmt.Errorf("error uploading config file %s: %w", file, err)
-                        }
-
-                        if _, err := client.RunSudo(fmt.Sprintf("mv %s %s", fileTmpPath, remotePath)); err != nil {
-                                return fmt.Errorf("error moving config file %s: %w", file, err)
-                        }
-
-                        if _, err := client.RunSudo(fmt.Sprintf("chown %s:%s %s", opts.Name, opts.Name, remotePath)); err != nil {
-                                return fmt.Errorf("error setting config file ownership %s: %w", file, err)
-                        }
-
-                        fmt.Printf("  Uploaded: %s\n", file)
-                }
-        }
-
-        fmt.Println("-> Creating environment file...")
-        envFilePath := fmt.Sprintf("/etc/ship/env/%s.env", opts.Name)
-        envContent := ""
-        for k, v := range opts.Env {
-                envContent += fmt.Sprintf("%s=%s\n", k, v)
-        }
-        if err := client.WriteSudoFile(envFilePath, envContent); err != nil {
-                return fmt.Errorf("error creating env file: %w", err)
-        }
-        if _, err := client.RunSudo(fmt.Sprintf("chmod 600 %s", envFilePath)); err != nil {
-                return fmt.Errorf("error setting env file permissions: %w", err)
-        }
-        if _, err := client.RunSudo(fmt.Sprintf("chown %s:%s %s", opts.Name, opts.Name, envFilePath)); err != nil {
-                return fmt.Errorf("error setting env file ownership: %w", err)
-        }
+var (
+        // Persistent flags
+        hostFlag string
 
-        fmt.Println("-> Creating systemd service...")
-        serviceContent, err := templates.SystemdService(map[string]string{
-                "Name":       opts.Name,
-                "User":       opts.Name,
-                "WorkDir":    workDir,
-                "BinaryPath": binaryDest,
-                "Port":       strconv.Itoa(port),
-                "EnvFile":    envFilePath,
-                "Args":       opts.Args,
-                "Memory":     opts.Memory,
-                "CPU":        opts.CPU,
-        })
-        if err != nil {
-                return fmt.Errorf("error generating systemd unit: %w", err)
-        }
-
-        servicePath := fmt.Sprintf("/etc/systemd/system/%s.service", opts.Name)
-        if err := client.WriteSudoFile(servicePath, serviceContent); err != nil {
-                return fmt.Errorf("error creating systemd unit: %w", err)
-        }
-
-        fmt.Println("-> Configuring Caddy...")
-        caddyContent, err := templates.AppCaddy(map[string]string{
-                "Domain": opts.Domain,
-                "Port":   strconv.Itoa(port),
-        })
-        if err != nil {
-                return fmt.Errorf("error generating Caddy config: %w", err)
-        }
-
-        caddyPath := fmt.Sprintf("/etc/caddy/sites-enabled/%s.caddy", opts.Name)
-        if err := client.WriteSudoFile(caddyPath, caddyContent); err != nil {
-                return fmt.Errorf("error creating Caddy config: %w", err)
-        }
-
-        fmt.Println("-> Reloading systemd...")
-        if _, err := client.RunSudo("systemctl daemon-reload"); err != nil {
-                return fmt.Errorf("error reloading systemd: %w", err)
-        }
-
-        fmt.Println("-> Starting service...")
-        if _, err := client.RunSudo(fmt.Sprintf("systemctl enable %s", opts.Name)); err != nil {
-                return fmt.Errorf("error enabling service: %w", err)
-        }
-        if _, err := client.RunSudo(fmt.Sprintf("systemctl restart %s", opts.Name)); err != nil {
-                return fmt.Errorf("error starting service: %w", err)
-        }
-
-        fmt.Println("-> Reloading Caddy...")
-        if _, err := client.RunSudo("systemctl reload caddy"); err != nil {
-                return fmt.Errorf("error reloading Caddy: %w", err)
-        }
-
-        st.AddApp(opts.Host, opts.Name, &state.App{
-                Type:   "app",
-                Domain: opts.Domain,
-                Port:   port,
-                Env:    opts.Env,
-                Args:   opts.Args,
-                Files:  opts.Files,
-                Memory: opts.Memory,
-                CPU:    opts.CPU,
-        })
-        if err := st.Save(); err != nil {
-                return fmt.Errorf("error saving state: %w", err)
-        }
-
-        fmt.Printf("\n App deployed successfully!\n")
-        // Show first domain in the URL message
-        primaryDomain := strings.Split(opts.Domain, ",")[0]
-        primaryDomain = strings.TrimSpace(primaryDomain)
-        fmt.Printf("  https://%s (may take a minute for HTTPS cert)\n", primaryDomain)
-        return nil
-}
-
-func updateAppConfig(st *state.State, opts DeployOptions) error {
-        existingApp, err := st.GetApp(opts.Host, opts.Name)
-        if err != nil {
-                return fmt.Errorf("app %s not found (use --binary to deploy a new app)", opts.Name)
-        }
-
-        if existingApp.Type != "app" {
-                return fmt.Errorf("%s is a static site, not an app", opts.Name)
-        }
-
-        fmt.Printf("Updating config: %s\n", opts.Name)
-
-        // Add PORT to env
-        opts.Env["PORT"] = strconv.Itoa(existingApp.Port)
-
-        client, err := ssh.Connect(opts.Host)
-        if err != nil {
-                return fmt.Errorf("error connecting to VPS: %w", err)
-        }
-        defer client.Close()
-
-        // Update env file
-        fmt.Println("-> Updating environment file...")
-        envFilePath := fmt.Sprintf("/etc/ship/env/%s.env", opts.Name)
-        envContent := ""
-        for k, v := range opts.Env {
-                envContent += fmt.Sprintf("%s=%s\n", k, v)
-        }
-        if err := client.WriteSudoFile(envFilePath, envContent); err != nil {
-                return fmt.Errorf("error creating env file: %w", err)
-        }
-
-        // Regenerate systemd unit
-        fmt.Println("-> Updating systemd service...")
-        workDir := fmt.Sprintf("/var/lib/%s", opts.Name)
-        binaryDest := fmt.Sprintf("/usr/local/bin/%s", opts.Name)
-        serviceContent, err := templates.SystemdService(map[string]string{
-                "Name":       opts.Name,
-                "User":       opts.Name,
-                "WorkDir":    workDir,
-                "BinaryPath": binaryDest,
-                "Port":       strconv.Itoa(existingApp.Port),
-                "EnvFile":    envFilePath,
-                "Args":       opts.Args,
-                "Memory":     opts.Memory,
-                "CPU":        opts.CPU,
-        })
-        if err != nil {
-                return fmt.Errorf("error generating systemd unit: %w", err)
-        }
-
-        servicePath := fmt.Sprintf("/etc/systemd/system/%s.service", opts.Name)
-        if err := client.WriteSudoFile(servicePath, serviceContent); err != nil {
-                return fmt.Errorf("error creating systemd unit: %w", err)
-        }
-
-        fmt.Println("-> Reloading systemd...")
-        if _, err := client.RunSudo("systemctl daemon-reload"); err != nil {
-                return fmt.Errorf("error reloading systemd: %w", err)
-        }
-
-        fmt.Println("-> Restarting service...")
-        if _, err := client.RunSudo(fmt.Sprintf("systemctl restart %s", opts.Name)); err != nil {
-                return fmt.Errorf("error restarting service: %w", err)
-        }
-
-        // Update state
-        existingApp.Args = opts.Args
-        existingApp.Memory = opts.Memory
-        existingApp.CPU = opts.CPU
-        existingApp.Env = opts.Env
-        if err := st.Save(); err != nil {
-                return fmt.Errorf("error saving state: %w", err)
-        }
-
-        fmt.Printf("\n Config updated successfully!\n")
-        return nil
-}
-
-func deployStatic(st *state.State, opts DeployOptions) error {
-        if _, err := os.Stat(opts.Dir); err != nil {
-                return fmt.Errorf("directory not found: %s", opts.Dir)
-        }
-
-        fmt.Printf("Deploying static site: %s\n", opts.Name)
-        fmt.Printf("  Domain(s): %s\n", opts.Domain)
-        fmt.Printf("  Directory: %s\n", opts.Dir)
-
-        if opts.IsUpdate {
-                fmt.Println("  Updating existing deployment")
-        }
-
-        client, err := ssh.Connect(opts.Host)
-        if err != nil {
-                return fmt.Errorf("error connecting to VPS: %w", err)
-        }
-        defer client.Close()
-
-        remoteDir := fmt.Sprintf("/var/www/%s", opts.Name)
-        fmt.Println("-> Creating remote directory...")
-        if _, err := client.RunSudo(fmt.Sprintf("mkdir -p %s", remoteDir)); err != nil {
-                return fmt.Errorf("error creating remote directory: %w", err)
-        }
-
-        currentUser, err := client.Run("whoami")
-        if err != nil {
-                return fmt.Errorf("error getting current user: %w", err)
-        }
-        currentUser = strings.TrimSpace(currentUser)
-
-        if _, err := client.RunSudo(fmt.Sprintf("chown -R %s:%s %s", currentUser, currentUser, remoteDir)); err != nil {
-                return fmt.Errorf("error setting temporary ownership: %w", err)
-        }
-
-        fmt.Println("-> Uploading files...")
-        if err := client.UploadDir(opts.Dir, remoteDir); err != nil {
-                return fmt.Errorf("error uploading files: %w", err)
-        }
-
-        fmt.Println("-> Setting permissions...")
-        if _, err := client.RunSudo(fmt.Sprintf("chown -R www-data:www-data %s", remoteDir)); err != nil {
-                return fmt.Errorf("error setting ownership: %w", err)
-        }
-        if _, err := client.RunSudo(fmt.Sprintf("chmod -R 755 %s", remoteDir)); err != nil {
-                return fmt.Errorf("error setting directory permissions: %w", err)
-        }
-        if _, err := client.RunSudo(fmt.Sprintf("find %s -type f -exec chmod 644 {} \\;", remoteDir)); err != nil {
-                return fmt.Errorf("error setting file permissions: %w", err)
-        }
-
-        fmt.Println("-> Configuring Caddy...")
-        caddyContent, err := templates.StaticCaddy(map[string]string{
-                "Domain":  opts.Domain,
-                "RootDir": remoteDir,
-        })
-        if err != nil {
-                return fmt.Errorf("error generating Caddy config: %w", err)
-        }
-
-        caddyPath := fmt.Sprintf("/etc/caddy/sites-enabled/%s.caddy", opts.Name)
-        if err := client.WriteSudoFile(caddyPath, caddyContent); err != nil {
-                return fmt.Errorf("error creating Caddy config: %w", err)
-        }
-
-        fmt.Println("-> Reloading Caddy...")
-        if _, err := client.RunSudo("systemctl reload caddy"); err != nil {
-                return fmt.Errorf("error reloading Caddy: %w", err)
-        }
-
-        st.AddApp(opts.Host, opts.Name, &state.App{
-                Type:   "static",
-                Domain: opts.Domain,
-        })
-        if err := st.Save(); err != nil {
-                return fmt.Errorf("error saving state: %w", err)
-        }
+        // Version info (set via ldflags)
+        version = "dev"
+        commit  = "none"
+        date    = "unknown"
+)
 
-        fmt.Printf("\n Static site deployed successfully!\n")
-        primaryDomain := strings.Split(opts.Domain, ",")[0]
-        primaryDomain = strings.TrimSpace(primaryDomain)
-        fmt.Printf("  https://%s (may take a minute for HTTPS cert)\n", primaryDomain)
-        return nil
+const banner = `
+        ~
+    ___|___
+   |   _   |
+  _|__|_|__|_
+ |   SHIP   |  Ship apps to your VPS
+  \_________/   with automatic HTTPS
+   ~~~~~~~~~
+`
+
+var rootCmd = &cobra.Command{
+        Use:   "ship",
+        Short: "Ship apps and static sites to a VPS with automatic HTTPS",
+        Long: banner + `
+A CLI tool for deploying applications and static sites to a VPS.
+
+How it works:
+  Ship uses only SSH to deploy - no agents, containers, or external services.
+  It uploads your binary or static website, creates a systemd service, and configures Caddy
+  for automatic HTTPS. Ports are assigned automatically. Your app runs directly on the VPS
+  with minimal overhead.
+
+Requirements:
+  • A VPS with SSH access (use 'ship host init' to set up a new server)
+  • An SSH config entry or user@host for your server
+  • A domain pointing to your VPS
+
+Examples:
+  # Deploy a Go binary
+  ship --binary ./myapp --domain api.example.com
+
+  # Deploy with auto-generated subdomain (requires base domain)
+  ship --binary ./myapp --name myapp
+
+  # Deploy a static site
+  ship --static --dir ./dist --domain example.com
+
+  # Update config without redeploying binary
+  ship --name myapp --memory 512M --cpu 50%
+  ship --name myapp --env DEBUG=true
+
+  # Set up a new VPS with base domain
+  ship host init --host user@vps --base-domain apps.example.com`,
+        RunE:          runDeploy,
+        SilenceUsage:  true,
+        SilenceErrors: true,
 }
 
-func parseEnvFile(path string) (map[string]string, error) {
-        file, err := os.Open(path)
-        if err != nil {
-                return nil, err
-        }
-        defer file.Close()
-
-        env := make(map[string]string)
-        scanner := bufio.NewScanner(file)
-        for scanner.Scan() {
-                line := strings.TrimSpace(scanner.Text())
-                if line == "" || strings.HasPrefix(line, "#") {
-                        continue
-                }
-
-                parts := strings.SplitN(line, "=", 2)
-                if len(parts) == 2 {
-                        env[parts[0]] = parts[1]
-                }
-        }
-
-        return env, scanner.Err()
+func init() {
+        // Persistent flags available to all subcommands
+        rootCmd.PersistentFlags().StringVar(&hostFlag, "host", "", "VPS host (SSH config alias or user@host)")
+
+        // Root command (deploy) flags
+        rootCmd.Flags().String("binary", "", "Path to Go binary (for app deployment)")
+        rootCmd.Flags().Bool("static", false, "Deploy as static site")
+        rootCmd.Flags().String("dir", ".", "Directory to deploy (for static sites)")
+        rootCmd.Flags().String("domain", "", "Custom domain (optional if base domain configured)")
+        rootCmd.Flags().String("name", "", "App name (default: inferred from binary or directory)")
+        rootCmd.Flags().Int("port", 0, "Port override (default: auto-allocate)")
+        rootCmd.Flags().StringArray("env", nil, "Environment variable (KEY=VALUE, can be specified multiple times)")
+        rootCmd.Flags().String("env-file", "", "Path to .env file")
+        rootCmd.Flags().String("args", "", "Arguments to pass to binary")
+        rootCmd.Flags().StringArray("file", nil, "Config file to upload to working directory (can be specified multiple times)")
+        rootCmd.Flags().String("memory", "", "Memory limit (e.g., 512M, 1G)")
+        rootCmd.Flags().String("cpu", "", "CPU limit (e.g., 50%, 200% for 2 cores)")
+
+        // Add subcommands
+        rootCmd.AddCommand(listCmd)
+        rootCmd.AddCommand(logsCmd)
+        rootCmd.AddCommand(statusCmd)
+        rootCmd.AddCommand(restartCmd)
+        rootCmd.AddCommand(removeCmd)
+        rootCmd.AddCommand(env.Cmd)
+        rootCmd.AddCommand(host.Cmd)
+        rootCmd.AddCommand(uiCmd)
+        rootCmd.AddCommand(versionCmd)
 }