diff --git a/cmd/docker-mcp/commands/catalog.go b/cmd/docker-mcp/commands/catalog.go
index eb3c20aa..12d83de9 100644
--- a/cmd/docker-mcp/commands/catalog.go
+++ b/cmd/docker-mcp/commands/catalog.go
@@ -13,12 +13,13 @@ import (
 	"github.com/docker/mcp-gateway/pkg/yq"
 )
 
-func catalogCommand(dockerCli command.Cli) *cobra.Command {
+func deprecatedCatalogCommand(dockerCli command.Cli) *cobra.Command {
 	cmd := &cobra.Command{
-		Use:     "catalog",
-		Aliases: []string{"catalogs"},
-		Short:   "Manage MCP server catalogs",
-		Long:    `Manage MCP server catalogs for organizing and configuring custom MCP servers alongside Docker's official catalog.`,
+		Use:     "catalog-deprecated",
+		Aliases: []string{"catalogs-deprecated"},
+		Short:   "Deprecated: Manage MCP server catalogs",
+		Long:    `Deprecated: Manage MCP server catalogs for organizing and configuring custom MCP servers alongside Docker's official catalog.`,
+		Hidden:  true,
 	}
 	cmd.AddCommand(bootstrapCatalogCommand())
 	cmd.AddCommand(importCatalogCommand())
diff --git a/cmd/docker-mcp/commands/catalog_next.go b/cmd/docker-mcp/commands/catalog_next.go
index 23162a6f..6b3c2fe6 100644
--- a/cmd/docker-mcp/commands/catalog_next.go
+++ b/cmd/docker-mcp/commands/catalog_next.go
@@ -13,10 +13,10 @@ import (
 	"github.com/docker/mcp-gateway/pkg/workingset"
 )
 
-func catalogNextCommand() *cobra.Command {
+func catalogCommand() *cobra.Command {
 	cmd := &cobra.Command{
-		Use:   "catalog-next",
-		Short: "Manage catalogs (next generation)",
+		Use:   "catalog",
+		Short: "Manage MCP server catalogs",
 	}
 
 	cmd.AddCommand(createCatalogNextCommand())
diff --git a/cmd/docker-mcp/commands/client.go b/cmd/docker-mcp/commands/client.go
index 04bea5a8..13e485ad 100644
--- a/cmd/docker-mcp/commands/client.go
+++ b/cmd/docker-mcp/commands/client.go
@@ -52,7 +52,7 @@ func connectClientCommand(dockerCli command.Cli, cwd string, cfg client.Config)
 		WorkingSet string
 	}
 	cmd := &cobra.Command{
-		Use:   fmt.Sprintf("connect [OPTIONS] <mcp-client>\n\nSupported clients: %s", strings.Join(client.GetSupportedMCPClients(cfg), " ")),
+		Use:   fmt.Sprintf("connect [OPTIONS] <mcp-client> --profile <profile-id>\n\nSupported clients: %s", strings.Join(client.GetSupportedMCPClients(cfg), " ")),
 		Short: fmt.Sprintf("Connect the Docker MCP Toolkit to a client. Supported clients: %s", strings.Join(client.GetSupportedMCPClients(cfg), " ")),
 		Args:  cobra.ExactArgs(1),
 		RunE: func(cmd *cobra.Command, args []string) error {
@@ -62,9 +62,8 @@ func connectClientCommand(dockerCli command.Cli, cwd string, cfg client.Config)
 	flags := cmd.Flags()
 	addGlobalFlag(flags, &opts.Global)
 	addQuietFlag(flags, &opts.Quiet)
-	if isWorkingSetsFeatureEnabled(dockerCli) {
-		addWorkingSetFlag(flags, &opts.WorkingSet)
-	}
+	_ = cmd.MarkFlagRequired(addWorkingSetFlag(flags, &opts.WorkingSet))
+
 	return cmd
 }
 
@@ -125,6 +124,7 @@ func addQuietFlag(flags *pflag.FlagSet, p *bool) {
 	flags.BoolVarP(p, "quiet", "q", false, "Only display errors.")
 }
 
-func addWorkingSetFlag(flags *pflag.FlagSet, p *string) {
+func addWorkingSetFlag(flags *pflag.FlagSet, p *string) string {
 	flags.StringVarP(p, "profile", "p", "", "Profile to use for client connection.")
+	return "profile"
 }
diff --git a/cmd/docker-mcp/commands/feature.go b/cmd/docker-mcp/commands/feature.go
index c12403e6..b6ea5b9d 100644
--- a/cmd/docker-mcp/commands/feature.go
+++ b/cmd/docker-mcp/commands/feature.go
@@ -40,7 +40,6 @@ Available features:
   oauth-interceptor      Enable GitHub OAuth flow interception for automatic authentication
   mcp-oauth-dcr          Enable Dynamic Client Registration (DCR) for automatic OAuth client setup
   dynamic-tools          Enable internal MCP management tools (mcp-find, mcp-add, mcp-remove)
-	profiles               Enable profile management (docker mcp profile <subcommand>)
   tool-name-prefix       Prefix all tool names with server name to avoid conflicts`,
 		Args: cobra.ExactArgs(1),
 		RunE: func(_ *cobra.Command, args []string) error {
@@ -48,7 +47,7 @@ Available features:
 
 			// Validate feature name
 			if !isKnownFeature(featureName) {
-				return fmt.Errorf("unknown feature: %s\n\nAvailable features:\n  oauth-interceptor      Enable GitHub OAuth flow interception\n  mcp-oauth-dcr          Enable Dynamic Client Registration for automatic OAuth setup\n  dynamic-tools          Enable internal MCP management tools\n  profiles               Enable profile management (docker mcp profile <subcommand>)\n  tool-name-prefix       Prefix all tool names with server name", featureName)
+				return fmt.Errorf("unknown feature: %s\n\nAvailable features:\n  oauth-interceptor      Enable GitHub OAuth flow interception\n  mcp-oauth-dcr          Enable Dynamic Client Registration for automatic OAuth setup\n  dynamic-tools          Enable internal MCP management tools\n  tool-name-prefix       Prefix all tool names with server name", featureName)
 			}
 
 			// Enable the feature
@@ -85,11 +84,6 @@ Available features:
 				fmt.Println("  - mcp-add: add MCP servers to the registry and reload configuration")
 				fmt.Println("  - mcp-remove: remove MCP servers from the registry and reload configuration")
 				fmt.Println("\nNo additional flags are needed - this applies to all gateway runs.")
-			case "profiles":
-				fmt.Println("\nThis feature enables profile management tools.")
-				fmt.Println("When enabled, the cli provides commands for managing profiles:")
-				fmt.Println("  - docker mcp profile <subcommand> ...")
-				fmt.Println("\nThis also enables the --profile flag for the docker mcp gateway run command.")
 			case "tool-name-prefix":
 				fmt.Println("\nThis feature enables automatic prefixing of tool names with server names.")
 				fmt.Println("When enabled, all tools are automatically prefixed with their server name:")
@@ -151,7 +145,7 @@ func featureListCommand(dockerCli command.Cli) *cobra.Command {
 			fmt.Println()
 
 			// Show all known features
-			knownFeatures := []string{"oauth-interceptor", "mcp-oauth-dcr", "dynamic-tools", "profiles", "tool-name-prefix"}
+			knownFeatures := []string{"oauth-interceptor", "mcp-oauth-dcr", "dynamic-tools", "tool-name-prefix"}
 			for _, feature := range knownFeatures {
 				status := "disabled"
 				if isFeatureEnabledFromCli(dockerCli, feature) {
@@ -168,8 +162,6 @@ func featureListCommand(dockerCli command.Cli) *cobra.Command {
 					fmt.Printf("  %-20s %s\n", "", "Enable Dynamic Client Registration (DCR) for automatic OAuth client setup")
 				case "dynamic-tools":
 					fmt.Printf("  %-20s %s\n", "", "Enable internal MCP management tools (mcp-find, mcp-add, mcp-remove)")
-				case "profiles":
-					fmt.Printf("  %-20s %s\n", "", "Enable profile management tools (docker mcp profile <subcommand>)")
 				case "tool-name-prefix":
 					fmt.Printf("  %-20s %s\n", "", "Prefix all tool names with server name to avoid conflicts")
 				}
@@ -240,7 +232,6 @@ func isKnownFeature(feature string) bool {
 		"oauth-interceptor",
 		"mcp-oauth-dcr",
 		"dynamic-tools",
-		"profiles",
 		"tool-name-prefix",
 	}
 
diff --git a/cmd/docker-mcp/commands/gateway.go b/cmd/docker-mcp/commands/gateway.go
index a7be957a..3ab33732 100644
--- a/cmd/docker-mcp/commands/gateway.go
+++ b/cmd/docker-mcp/commands/gateway.go
@@ -47,11 +47,7 @@ func gatewayCommand(docker docker.Client, dockerCli command.Cli) *cobra.Command
 	} else {
 		// On-host.
 		options = gateway.Config{
-			CatalogPath:  []string{catalog.DockerCatalogFilename},
-			RegistryPath: []string{"registry.yaml"},
-			ConfigPath:   []string{"config.yaml"},
-			ToolsPath:    []string{"tools.yaml"},
-			SecretsPath:  "docker-desktop",
+			SecretsPath: "docker-desktop",
 			Options: gateway.Options{
 				Cpus:         1,
 				Memory:       "2Gb",
@@ -68,6 +64,22 @@ func gatewayCommand(docker docker.Client, dockerCli command.Cli) *cobra.Command
 		Short: "Run the gateway",
 		Args:  cobra.NoArgs,
 		RunE: func(cmd *cobra.Command, _ []string) error {
+			if len(options.CatalogPath) == 0 && len(options.RegistryPath) == 0 && len(options.ConfigPath) == 0 && len(options.ToolsPath) == 0 {
+				// We're in working set mode, so use the default profile if no profile is specified
+				if options.WorkingSet == "" {
+					options.WorkingSet = "default"
+				}
+			}
+
+			if options.WorkingSet != "" &&
+				(len(options.ServerNames) > 0 || enableAllServers ||
+					len(options.CatalogPath) > 0 || len(options.RegistryPath) > 0 || len(options.ConfigPath) > 0 || len(options.ToolsPath) > 0 ||
+					len(additionalCatalogs) > 0 || len(additionalRegistries) > 0 || len(additionalConfigs) > 0 || len(additionalToolsConfig) > 0 ||
+					len(mcpRegistryUrls) > 0 || len(options.OciRef) > 0 ||
+					options.SecretsPath != "docker-desktop") {
+				return fmt.Errorf("cannot use --profile with --servers, --enable-all-servers, --catalog, --additional-catalog, --registry, --additional-registry, --config, --additional-config, --tools-config, --additional-tools-config, --secrets, --oci-ref, --mcp-registry flags")
+			}
+
 			// Check if OAuth interceptor feature is enabled
 			options.OAuthInterceptorEnabled = isOAuthInterceptorFeatureEnabled(dockerCli)
 
@@ -123,15 +135,6 @@ func gatewayCommand(docker docker.Client, dockerCli command.Cli) *cobra.Command
 				options.MCPRegistryServers = mcpServers
 			}
 
-			if options.WorkingSet != "" {
-				if len(options.ServerNames) > 0 {
-					return fmt.Errorf("cannot use --profile with --servers flag")
-				}
-				if enableAllServers {
-					return fmt.Errorf("cannot use --profile with --enable-all-servers flag")
-				}
-			}
-
 			// Handle --enable-all-servers flag
 			if enableAllServers {
 				if len(options.ServerNames) > 0 {
@@ -169,9 +172,7 @@ func gatewayCommand(docker docker.Client, dockerCli command.Cli) *cobra.Command
 	}
 
 	runCmd.Flags().StringSliceVar(&options.ServerNames, "servers", nil, "Names of the servers to enable (if non empty, ignore --registry flag)")
-	if isWorkingSetsFeatureEnabled(dockerCli) {
-		runCmd.Flags().StringVar(&options.WorkingSet, "profile", "", "Profile ID to use (mutually exclusive with --servers and --enable-all-servers)")
-	}
+	runCmd.Flags().StringVar(&options.WorkingSet, "profile", options.WorkingSet, "Profile ID to use (incompatible with --servers, --enable-all-servers, --catalog, --registry, --config, --tools-config, --secrets, --oci-ref, --mcp-registry)")
 	runCmd.Flags().BoolVar(&enableAllServers, "enable-all-servers", false, "Enable all servers in the catalog (instead of using individual --servers options)")
 	runCmd.Flags().StringSliceVar(&options.CatalogPath, "catalog", options.CatalogPath, "Paths to docker catalogs (absolute or relative to ~/.docker/mcp/catalogs/)")
 	runCmd.Flags().StringSliceVar(&additionalCatalogs, "additional-catalog", nil, "Additional catalog paths to append to the default catalogs")
@@ -345,17 +346,3 @@ func isToolNamePrefixFeatureEnabled(dockerCli command.Cli) bool {
 
 	return value == "enabled"
 }
-
-// isWorkingSetsFeatureEnabled checks if the profiles feature is enabled
-func isWorkingSetsFeatureEnabled(dockerCli command.Cli) bool {
-	configFile := dockerCli.ConfigFile()
-	if configFile == nil || configFile.Features == nil {
-		return false
-	}
-
-	value, exists := configFile.Features["profiles"]
-	if !exists {
-		return false
-	}
-	return value == "enabled"
-}
diff --git a/cmd/docker-mcp/commands/root.go b/cmd/docker-mcp/commands/root.go
index 032c59d6..c54cbd7b 100644
--- a/cmd/docker-mcp/commands/root.go
+++ b/cmd/docker-mcp/commands/root.go
@@ -70,11 +70,9 @@ func Root(ctx context.Context, cwd string, dockerCli command.Cli) *cobra.Command
 
 	dockerClient := docker.NewClient(dockerCli)
 
-	if isWorkingSetsFeatureEnabled(dockerCli) {
-		cmd.AddCommand(workingSetCommand())
-		cmd.AddCommand(catalogNextCommand())
-	}
-	cmd.AddCommand(catalogCommand(dockerCli))
+	cmd.AddCommand(workingSetCommand())
+	cmd.AddCommand(catalogCommand())
+	cmd.AddCommand(deprecatedCatalogCommand(dockerCli))
 	cmd.AddCommand(clientCommand(dockerCli, cwd))
 	cmd.AddCommand(configCommand(dockerClient))
 	cmd.AddCommand(featureCommand(dockerCli))
diff --git a/cmd/docker-mcp/commands/workingset.go b/cmd/docker-mcp/commands/workingset.go
index f30576cf..ae69ae73 100644
--- a/cmd/docker-mcp/commands/workingset.go
+++ b/cmd/docker-mcp/commands/workingset.go
@@ -20,7 +20,7 @@ func workingSetCommand() *cobra.Command {
 
 	cmd := &cobra.Command{
 		Use:   "profile",
-		Short: "Manage profiles",
+		Short: "Manage MCP profiles",
 	}
 
 	cmd.AddCommand(exportWorkingSetCommand())
diff --git a/docs/catalog.md b/docs/catalog.md
index 9cbaa7ff..ceb01383 100644
--- a/docs/catalog.md
+++ b/docs/catalog.md
@@ -1,5 +1,7 @@
 # MCP Catalog Management
 
+*Important note: This method of catalog management is deprecated. Please see [Profiles](profiles.md) for more information on how to use catalogs.*
+
 Docker MCP Gateway provides comprehensive catalog management capabilities, allowing you to create, manage, and use custom MCP server catalogs alongside Docker's official catalog.
 
 ## Quick Start with Bootstrap
@@ -8,7 +10,7 @@ The easiest way to get started with custom catalogs is to use the `bootstrap` co
 
 ```bash
 # Create a starter catalog with Docker Hub and Docker CLI server examples
-docker mcp catalog bootstrap ./my-starter-catalog.yaml
+docker mcp catalog-deprecated bootstrap ./my-starter-catalog.yaml
 
 # The file now contains properly formatted server definitions you can modify
 ```
@@ -25,17 +27,17 @@ This creates a YAML file with real server definitions that you can:
 
 ```bash
 # List all configured catalogs
-docker mcp catalog ls
+docker mcp catalog-deprecated ls
 
 # List in JSON format
-docker mcp catalog ls --format=json
+docker mcp catalog-deprecated ls --format=json
 ```
 
 ### Creating Catalogs
 
 ```bash
 # Create a new empty catalog
-docker mcp catalog create my-custom-catalog
+docker mcp catalog-deprecated create my-custom-catalog
 
 # The catalog is now ready for adding servers
 ```
@@ -44,62 +46,62 @@ docker mcp catalog create my-custom-catalog
 
 ```bash
 # Show servers in the default Docker catalog
-docker mcp catalog show
+docker mcp catalog-deprecated show
 
 # Show servers in a specific catalog
-docker mcp catalog show my-custom-catalog
+docker mcp catalog-deprecated show my-custom-catalog
 
 # Show in different formats
-docker mcp catalog show docker-mcp --format json
-docker mcp catalog show docker-mcp --format yaml
+docker mcp catalog-deprecated show docker-mcp --format json
+docker mcp catalog-deprecated show docker-mcp --format yaml
 ```
 
 ### Adding Servers to Catalogs
 
 ```bash
 # Add a server from another catalog file
-docker mcp catalog add my-custom-catalog server-name ./source-catalog.yaml
+docker mcp catalog-deprecated add my-custom-catalog server-name ./source-catalog.yaml
 
 # Force overwrite if server already exists
-docker mcp catalog add my-custom-catalog server-name ./source-catalog.yaml --force
+docker mcp catalog-deprecated add my-custom-catalog server-name ./source-catalog.yaml --force
 ```
 
 ### Importing Servers from OSS MCP Community Registry
 
 ```bash
 # replace {id} in the url below
-docker mcp catalog import my-custom-catalog --mcp-registry https://registry.modelcontextprotocol.io/v0/servers/{id}
+docker mcp catalog-deprecated import my-custom-catalog --mcp-registry https://registry.modelcontextprotocol.io/v0/servers/{id}
 ```
 
 ### Importing Other Catalogs
 
 ```bash
 # Import a catalog from a local file
-docker mcp catalog import ./my-catalog.yaml
+docker mcp catalog-deprecated import ./my-catalog.yaml
 
 # Import from a URL
-docker mcp catalog import https://example.com/catalog.yaml
+docker mcp catalog-deprecated import https://example.com/catalog.yaml
 
 # Import with an alias
-docker mcp catalog import team-servers
+docker mcp catalog-deprecated import team-servers
 ```
 
 ### Exporting Catalogs
 
 ```bash
 # Export a custom catalog to a file
-docker mcp catalog export my-custom-catalog ./backup.yaml
+docker mcp catalog-deprecated export my-custom-catalog ./backup.yaml
 
 # Note: You cannot export Docker's official catalog
-docker mcp catalog export docker-mcp ./docker-backup.yaml
-# Error: Cannot export the Docker MCP catalog as it is managed by Docker
+docker mcp catalog-deprecated export docker-mcp ./docker-backup.yaml
+# Error: Cannot export the Docker MCP catalog-deprecated as it is managed by Docker
 ```
 
 ### Forking Catalogs
 
 ```bash
 # Create a copy of an existing catalog
-docker mcp catalog fork docker-mcp my-custom-version
+docker mcp catalog-deprecated fork docker-mcp my-custom-version
 
 # Now you can modify my-custom-version independently
 ```
@@ -108,7 +110,7 @@ docker mcp catalog fork docker-mcp my-custom-version
 
 ```bash
 # Remove a custom catalog
-docker mcp catalog rm my-custom-catalog
+docker mcp catalog-deprecated rm my-custom-catalog
 
 # Note: You cannot remove Docker's official catalog
 ```
@@ -117,17 +119,17 @@ docker mcp catalog rm my-custom-catalog
 
 ```bash
 # Update all catalogs
-docker mcp catalog update
+docker mcp catalog-deprecated update
 
 # Update a specific catalog
-docker mcp catalog update my-custom-catalog
+docker mcp catalog-deprecated update my-custom-catalog
 ```
 
 ### Resetting Catalogs
 
 ```bash
 # Remove all custom catalogs and reset to Docker defaults
-docker mcp catalog reset
+docker mcp catalog-deprecated reset
 ```
 
 ## Catalog YAML Format
@@ -255,13 +257,13 @@ registry:
 
 ```bash
 # 1. Create a starter catalog for reference
-docker mcp catalog bootstrap ./starter-catalog.yaml
+docker mcp catalog-deprecated bootstrap ./starter-catalog.yaml
 
 # 2. Create your own catalog
-docker mcp catalog create dev-servers
+docker mcp catalog-deprecated create dev-servers
 
 # 3. Add useful servers from the starter (optional)
-docker mcp catalog add dev-servers dockerhub ./starter-catalog.yaml
+docker mcp catalog-deprecated add dev-servers dockerhub ./starter-catalog.yaml
 
 # 4. Create a custom server definition file
 cat > my-server.yaml << EOF
@@ -276,35 +278,35 @@ registry:
 EOF
 
 # 5. Add your custom server
-docker mcp catalog add dev-servers my-dev-server ./my-server.yaml
+docker mcp catalog-deprecated add dev-servers my-dev-server ./my-server.yaml
 ```
 
 ### Importing from the OSS MCP Community Registry
 
 ```bash
 # 1. Create a destination catalog for your community servers
-docker mcp catalog create community-catalog
+docker mcp catalog-deprecated create community-catalog
 
 # 2. import the OSS MCP community server resource
-docker mcp catalog import --mcp-registry http://registry.modelcontextprotocol.io/v0/servers/71de5a2a-6cfb-4250-a196-f93080ecc860
+docker mcp catalog-deprecated import --mcp-registry http://registry.modelcontextprotocol.io/v0/servers/71de5a2a-6cfb-4250-a196-f93080ecc860
 
 # 3. show the imported server
-docker mcp catalog show community-catalog --format=json | jq .
+docker mcp catalog-deprecated show community-catalog --format=json | jq .
 ```
 
 ### Team Sharing Workflow
 
 ```bash
 # Team lead: Create and export a team catalog
-docker mcp catalog create team-servers
-docker mcp catalog add team-servers shared-db ./shared-db-server.yaml
-docker mcp catalog add team-servers api-helper ./api-helper-server.yaml
-docker mcp catalog export team-servers ./team-catalog.yaml
+docker mcp catalog-deprecated create team-servers
+docker mcp catalog-deprecated add team-servers shared-db ./shared-db-server.yaml
+docker mcp catalog-deprecated add team-servers api-helper ./api-helper-server.yaml
+docker mcp catalog-deprecated export team-servers ./team-catalog.yaml
 
 # Share team-catalog.yaml with team members
 
 # Team members: Import the shared catalog
-docker mcp catalog import ./team-catalog.yaml
+docker mcp catalog-deprecated import ./team-catalog.yaml
 docker mcp gateway run
 ```
 
@@ -312,30 +314,30 @@ docker mcp gateway run
 
 ```bash
 # 1. Create a test catalog
-docker mcp catalog create test-servers
+docker mcp catalog-deprecated create test-servers
 
 # 2. Add your server for testing
-docker mcp catalog add test-servers test-server ./test-server.yaml
+docker mcp catalog-deprecated add test-servers test-server ./test-server.yaml
 
 # 3. Run gateway with test catalog
 docker mcp gateway run
 
 # 4. When done testing, clean up
-docker mcp catalog rm test-servers
+docker mcp catalog-deprecated rm test-servers
 ```
 
 ### Production Deployment
 
 ```bash
 # 1. Create production catalog
-docker mcp catalog create prod-servers
+docker mcp catalog-deprecated create prod-servers
 
 # 2. Add only production-ready servers
-docker mcp catalog add prod-servers monitoring ./monitoring-server.yaml
-docker mcp catalog add prod-servers logging ./logging-server.yaml
+docker mcp catalog-deprecated add prod-servers monitoring ./monitoring-server.yaml
+docker mcp catalog-deprecated add prod-servers logging ./logging-server.yaml
 
 # 3. Export for backup and deployment
-docker mcp catalog export prod-servers ./prod-catalog-backup.yaml
+docker mcp catalog-deprecated export prod-servers ./prod-catalog-backup.yaml
 
 # 4. Deploy with production catalog
 docker mcp gateway run
@@ -375,7 +377,7 @@ Error: server "server-name" not found in catalog "source.yaml"
 
 ### Cannot Export Docker Catalog
 ```bash
-Error: cannot export the Docker MCP catalog as it is managed by Docker
+Error: cannot export the Docker MCP catalog-deprecated as it is managed by Docker
 ```
 **Solution**: This is intentional - Docker's catalog cannot be exported. Use `bootstrap` to get Docker server examples instead.
 
diff --git a/docs/mcp-gateway.md b/docs/mcp-gateway.md
index 8ea4ee22..9f7af02f 100644
--- a/docs/mcp-gateway.md
+++ b/docs/mcp-gateway.md
@@ -9,29 +9,23 @@ See [Why running MCP Servers in Container is more secure](security.md)
 Start up an MCP Gateway. This can be used for one client, or to service multiple clients if using either `sse` or `streaming` transports.
 
 ```bash
-# Run the MCP gateway (stdio)
+# Run with a profile (stdio)
+docker mcp gateway run --profile my-profile
+
+# Run the MCP gateway (stdio) - uses the profile with ID "default"
 docker mcp gateway run
 
 # Run the MCP gateway (streaming)
-docker mcp gateway run --port 8080 --transport streaming
-
-# Run with specific servers only, and select all tools from server1 and just tool2 from server2
-docker mcp gateway run --servers server1,server2 --tools server1:* --tools server2:tool2
-
-# Run a fallback secret lookup - lookup desktop secret first and the fallback to a local .env file
-docker mcp gateway run --secrets=docker-desktop:./.env
+docker mcp gateway run --profile my-profile --port 8080 --transport streaming
 
 # Run with verbose logging
-docker mcp gateway run --verbose --log-calls
+docker mcp gateway run  --profile my-profile --verbose --log-calls
 
 # Run in watch mode (auto-reload on config changes)
-docker mcp gateway run --watch
+docker mcp gateway run --profile my-profile --watch
 
 # Run a standalone dockerized MCP server (no catalog required)
 docker mcp gateway run --server docker.io/namespace/repository:latest
-
-# Run with a profile (requires profiles feature to be enabled)
-docker mcp gateway run --profile my-working-set
 ```
 
 See [Profiles](profiles.md) for more information about organizing servers into reusable collections.
@@ -45,7 +39,7 @@ A typical usage looks like this Claude Desktop configuration:
     "mcpServers": {
         "MCP_DOCKER": {
             "command": "docker",
-            "args": ["mcp", "gateway", "run"]
+            "args": ["mcp", "gateway", "run", "--profile", "my-profile"]
         }
     }
 }
@@ -53,6 +47,8 @@ A typical usage looks like this Claude Desktop configuration:
 
 ## How to run the MCP Gateway with Docker Compose?
 
+*Note: This is using a deprecated method of working with the gateway. Profile support in compose is coming soon.*
+
 The simplest way to tun the MCP Gateway with Docker Compose is with this kind of compose file:
 
 ```
@@ -61,8 +57,10 @@ services:
     image: docker/mcp-gateway
     command:
       - --servers=duckduckgo
+      - --catalog=/mcp/catalog.yaml
     volumes:
       - /var/run/docker.sock:/var/run/docker.sock
+      - ./catalog.yaml:/mcp/catalog.yaml
 ```
 
 ### What does it do?
@@ -90,6 +88,7 @@ Docker MCP Toolkit's CLI - Manage your MCP servers and clients.
 Usage: docker mcp gateway run
 
 Flags:
+      --profile string                    Profile ID to use (incompatible with --servers, --enable-all-servers, --catalog, --registry, --config, --tools-config, --secrets, --oci-ref, --mcp-registry)
       --block-network             Block tools from accessing forbidden network resources
       --block-secrets             Block secrets from being/received sent to/from tools (default true)
       --catalog string            path to the docker-mcp.yaml catalog (absolute or relative to ~/.docker/mcp/catalogs/) (default "docker-mcp.yaml")
@@ -109,11 +108,8 @@ Flags:
       --verbose                   Verbose output
       --verify-signatures         Verify signatures of the server images
       --watch                     Watch for changes and reconfigure the gateway (default true)
-      --profile string            Profile ID to use (requires working-sets feature, mutually exclusive with --servers and --enable-all-servers)
 ```
 
-**Note:** The `--profile` flag is only available when the `profiles` feature is enabled via `docker mcp feature enable profiles`.
-
 ## Troubleshooting
 
 Look at our [Troubleshooting Guide](/docs/troubleshooting.md)
diff --git a/docs/profiles.md b/docs/profiles.md
index 8314c1c7..a8707f7e 100644
--- a/docs/profiles.md
+++ b/docs/profiles.md
@@ -615,11 +615,11 @@ docker mcp profile pull docker.io/myorg/my-tools:1.1
 
 ```bash
 # 1. Import Docker's official catalog (or pull from OCI registry)
-docker mcp catalog-next create docker-mcp-catalog \
+docker mcp catalog create docker-mcp-catalog \
   --from-legacy-catalog https://desktop.docker.com/mcp/catalog/v3/catalog.json
 
 # Or pull a team catalog from OCI registry
-docker mcp catalog-next pull myorg/team-catalog:latest
+docker mcp catalog pull myorg/team-catalog:latest
 
 # 2. Create an initial profile
 docker mcp profile create --name my-workflow
@@ -801,7 +801,7 @@ Error: server 'nonexistent' not found in catalog
 ```
 
 **Solution**: 
-- Use `docker mcp catalog-next show <catalog-name>` to see available servers in the catalog
+- Use `docker mcp catalog show <catalog-name>` to see available servers in the catalog
 - Check that the server name is spelled correctly (names are case-sensitive)
 
 ### Cannot Remove Server
@@ -868,36 +868,36 @@ Error: tool 'invalid_tool' not found in server 'github'
 
 ## Creating Catalogs from Profiles
 
-The `catalog-next` command allows you to create and share catalogs:
+The `catalog` command allows you to create and share catalogs:
 
 ```bash
 # Create a catalog from a working set
-docker mcp catalog-next create my-catalog --from-profile my-profile
+docker mcp catalog create my-catalog --from-profile my-profile
 
 # Create with a custom name
-docker mcp catalog-next create my-catalog --from-profile my-profile --name "My Catalog"
+docker mcp catalog create my-catalog --from-profile my-profile --name "My Catalog"
 
 # Create a catalog from a legacy catalog
-docker mcp catalog-next create docker-mcp-catalog --from-legacy-catalog https://desktop.docker.com/mcp/catalog/v3/catalog.json
+docker mcp catalog create docker-mcp-catalog --from-legacy-catalog https://desktop.docker.com/mcp/catalog/v3/catalog.json
 
 # List all catalogs
-docker mcp catalog-next list
+docker mcp catalog list
 
 # Show catalog details
-docker mcp catalog-next show my-catalog
+docker mcp catalog show my-catalog
 
 # Show a catalog, pulling it if missing (other options include 'never' and 'always')
-docker mcp catalog-next show mcp/docker-mcp-catalog --pull missing
+docker mcp catalog show mcp/docker-mcp-catalog --pull missing
 
 # Remove a catalog
-docker mcp catalog-next remove my-catalog
+docker mcp catalog remove my-catalog
 
 # Push catalog to OCI registry
-docker mcp catalog-next tag my-catalog my-org/my-catalog:latest
-docker mcp catalog-next push myorg/my-catalog:latest
+docker mcp catalog tag my-catalog my-org/my-catalog:latest
+docker mcp catalog push myorg/my-catalog:latest
 
 # Pull catalog from OCI registry
-docker mcp catalog-next pull myorg/my-catalog:latest
+docker mcp catalog pull myorg/my-catalog:latest
 ```
 
 **Key points:**
@@ -909,7 +909,7 @@ docker mcp catalog-next pull myorg/my-catalog:latest
 
 **💡 Tip:** You can import Docker's official MCP catalog as a starting point:
 ```bash
-docker mcp catalog-next create docker-mcp-catalog \
+docker mcp catalog create docker-mcp-catalog \
   --from-legacy-catalog https://desktop.docker.com/mcp/catalog/v3/catalog.json
 ```
 This gives you access to Docker's curated collection of MCP servers, which you can then use to build your profiles with the `--server catalog://docker-mcp-catalog/<server>` flag
diff --git a/docs/troubleshooting.md b/docs/troubleshooting.md
index 5672ef99..c4299cc8 100644
--- a/docs/troubleshooting.md
+++ b/docs/troubleshooting.md
@@ -8,7 +8,7 @@ What can you do to pinpoint where the problem comes from?
 The go to command to start a fresh Gateway, plugged into Docker Desltop's Toolkit is this one:
 
 ```console
-docker mcp gateway run --verbose --dry-run
+docker mcp gateway run --profile my-profile --verbose --dry-run
 ```
 
 This will show you how the Gateway is reading the configuration, which servers are actually
@@ -19,12 +19,6 @@ It'll show you how many tools you have, in aggregate.
 This is usually a good way to troubleshoot missing images, invalid server names, missing config
 or secrets...
 
-You can also focus a one given server with:
-
-```console
-docker mcp gateway run --verbose --dry-run --servers=duckduckgo
-```
-
 ## Debug tool calls
 
 Full fledge MCP clients might sometimes hide the errors they encounter while calling tools
diff --git a/pkg/catalog_next/list.go b/pkg/catalog_next/list.go
index ceaba323..2c8d4227 100644
--- a/pkg/catalog_next/list.go
+++ b/pkg/catalog_next/list.go
@@ -19,7 +19,7 @@ func List(ctx context.Context, dao db.DAO, format workingset.OutputFormat) error
 	}
 
 	if len(dbCatalogs) == 0 && format == workingset.OutputFormatHumanReadable {
-		fmt.Println("No catalogs found. Use `docker mcp catalog-next create` or `docker mcp catalog-next pull <oci-reference>` to create a catalog.")
+		fmt.Println("No catalogs found. Use `docker mcp catalog create` or `docker mcp catalog pull <oci-reference>` to create a catalog.")
 		return nil
 	}
 
diff --git a/pkg/catalog_next/list_test.go b/pkg/catalog_next/list_test.go
index 935d8bbc..dbdcfbbd 100644
--- a/pkg/catalog_next/list_test.go
+++ b/pkg/catalog_next/list_test.go
@@ -41,7 +41,7 @@ func TestListEmpty(t *testing.T) {
 	})
 
 	assert.Contains(t, output, "No catalogs found")
-	assert.Contains(t, output, "docker mcp catalog-next create")
+	assert.Contains(t, output, "docker mcp catalog create")
 }
 
 func TestListHumanReadable(t *testing.T) {
diff --git a/pkg/client/config.go b/pkg/client/config.go
index 3cf7833c..5b034be8 100644
--- a/pkg/client/config.go
+++ b/pkg/client/config.go
@@ -63,8 +63,8 @@ func FindGitProjectRoot(dir string) string {
 
 func GetSupportedMCPClients(cfg Config) []string {
 	tmp := map[string]struct{}{
-		VendorGordon: {},
-		VendorCodex:  {},
+		// Gordon is not supported for profiles yet
+		VendorCodex: {},
 	}
 	for k := range cfg.System {
 		tmp[k] = struct{}{}
diff --git a/pkg/client/connect.go b/pkg/client/connect.go
index f82d1fc2..e8407679 100644
--- a/pkg/client/connect.go
+++ b/pkg/client/connect.go
@@ -9,22 +9,17 @@ import (
 var ErrCodexOnlySupportsGlobalConfiguration = errors.New("codex only supports global configuration. Re-run with --global or -g")
 
 func Connect(ctx context.Context, cwd string, config Config, vendor string, global bool, workingSet string) error {
-	if vendor == VendorCodex {
+	switch vendor {
+	case VendorCodex:
 		if !global {
 			return ErrCodexOnlySupportsGlobalConfiguration
 		}
 		if err := ConnectCodex(ctx, workingSet); err != nil {
 			return err
 		}
-	} else if vendor == VendorGordon && global {
-		if workingSet != "" {
-			// Gordon doesn't support profiles yet
-			return fmt.Errorf("gordon cannot be connected to a profile")
-		}
-		if err := ConnectGordon(ctx); err != nil {
-			return err
-		}
-	} else {
+	case VendorGordon:
+		return fmt.Errorf("gordon support for profiles is not yet implemented")
+	default:
 		updater, err := getUpdater(vendor, global, cwd, config)
 		if err != nil {
 			return err