diff --git a/.goreleaser.yaml b/cli/.goreleaser.yaml
similarity index 100%
rename from .goreleaser.yaml
rename to cli/.goreleaser.yaml
diff --git a/client/chatGPT_client.go b/cli/client/chatGPT_client.go
similarity index 100%
rename from client/chatGPT_client.go
rename to cli/client/chatGPT_client.go
diff --git a/client/flink_client.go b/cli/client/flink_client.go
similarity index 100%
rename from client/flink_client.go
rename to cli/client/flink_client.go
diff --git a/client/flink_client_test.go b/cli/client/flink_client_test.go
similarity index 100%
rename from client/flink_client_test.go
rename to cli/client/flink_client_test.go
diff --git a/client/flink_ui_client.go b/cli/client/flink_ui_client.go
similarity index 100%
rename from client/flink_ui_client.go
rename to cli/client/flink_ui_client.go
diff --git a/client/gemini_client.go b/cli/client/gemini_client.go
similarity index 100%
rename from client/gemini_client.go
rename to cli/client/gemini_client.go
diff --git a/client/network_chains.go b/cli/client/network_chains.go
similarity index 100%
rename from client/network_chains.go
rename to cli/client/network_chains.go
diff --git a/client/network_chains_test.go b/cli/client/network_chains_test.go
similarity index 100%
rename from client/network_chains_test.go
rename to cli/client/network_chains_test.go
diff --git a/commands/chat_manuscript.go b/cli/commands/chat_manuscript.go
similarity index 100%
rename from commands/chat_manuscript.go
rename to cli/commands/chat_manuscript.go
diff --git a/commands/commander.go b/cli/commands/commander.go
similarity index 92%
rename from commands/commander.go
rename to cli/commands/commander.go
index da56a1a..6045e00 100644
--- a/commands/commander.go
+++ b/cli/commands/commander.go
@@ -2,7 +2,6 @@ package commands
 
 import (
 	"fmt"
-	"log"
 	"manuscript-core/pkg"
 	"os"
 
@@ -49,7 +48,7 @@ You'll be prompted to select:
 }
 
 var jobListCmd = &cobra.Command{
-	Use:     "list [directory]",
+	Use:     "list",
 	Aliases: []string{"ls"},
 	Short:   "List all manuscript jobs",
 	Long: `📋 View all running manuscript jobs
@@ -71,20 +70,13 @@ Usage:
 - Specify a directory path to check manuscripts in that location`,
 	Example: `>> manuscript-cli ls
 >> manuscript-cli list /path/to/manuscripts`,
-	Args: cobra.MaximumNArgs(1),
+	Args: cobra.MaximumNArgs(0),
 	Run: func(cmd *cobra.Command, args []string) {
-		var dir string
-		// if no args, use default manuscript directory
-		if len(args) == 0 {
-			config, err := pkg.LoadConfig(manuscriptConfig)
-			if err != nil {
-				log.Fatalf("Error: Failed to load config: %v", err)
-			}
-			dir = fmt.Sprintf("%s/%s", config.BaseDir, manuscriptBaseName)
-		} else {
-			dir = args[0] // use specified directory if user input
+		config, err := pkg.LoadConfig(manuscriptConfig)
+		if err != nil {
+			fmt.Println("Error: Failed to load manuscript config: %v", err)
 		}
-		ListJobs(dir)
+		ListJobs(config)
 	},
 }
 
diff --git a/commands/deploy_manuscript.go b/cli/commands/deploy_manuscript.go
similarity index 100%
rename from commands/deploy_manuscript.go
rename to cli/commands/deploy_manuscript.go
diff --git a/commands/help_template.go b/cli/commands/help_template.go
similarity index 100%
rename from commands/help_template.go
rename to cli/commands/help_template.go
diff --git a/commands/init_manuscript.go b/cli/commands/init_manuscript.go
similarity index 99%
rename from commands/init_manuscript.go
rename to cli/commands/init_manuscript.go
index d2d6dbd..fbf027b 100644
--- a/commands/init_manuscript.go
+++ b/cli/commands/init_manuscript.go
@@ -18,7 +18,7 @@ import (
 )
 
 const (
-	manuscriptBaseName   = "manuscript"
+	manuscriptBaseName   = "manuscripts"
 	manuscriptBaseDir    = "$HOME"
 	manuscriptConfig     = "$HOME/.manuscript_config.ini"
 	networkChainURL      = "https://api.chainbase.com"
diff --git a/commands/init_manuscript_test.go b/cli/commands/init_manuscript_test.go
similarity index 100%
rename from commands/init_manuscript_test.go
rename to cli/commands/init_manuscript_test.go
diff --git a/commands/jobs_manuscript.go b/cli/commands/jobs_manuscript.go
similarity index 94%
rename from commands/jobs_manuscript.go
rename to cli/commands/jobs_manuscript.go
index 76e8c65..9daa855 100644
--- a/commands/jobs_manuscript.go
+++ b/cli/commands/jobs_manuscript.go
@@ -41,7 +41,7 @@ func formatDurationToMinutes(durationMs int64) string {
 	return fmt.Sprintf("%d minutes", durationMinutes)
 }
 
-func ListJobs(dir string) {
+func ListJobs(config *pkg.Config) {
 	_ = pkg.ExecuteStepWithLoading("Checking jobs", false, func() error {
 		// Step 1: Check for running Docker containers
 		dockers, err := getRunningContainers()
@@ -54,21 +54,8 @@ func ListJobs(dir string) {
 			fmt.Println("\r📍 There are no jobs running...")
 		}
 
-		// Step 2: Get manuscripts based on source (config or directory)
-		manuscripts, err := getManuscripts(dir)
-		if err != nil {
-			return fmt.Errorf("failed to get manuscripts: %w", err)
-		}
-
-		if len(manuscripts) == 0 {
-			if dir != "" {
-				fmt.Printf("\r⚠️ No manuscript files found in %s\n", dir)
-			}
-			return nil
-		}
-
 		// Step 3: Check and display state for each manuscript
-		displayManuscriptStates(manuscripts, dockers)
+		displayManuscriptStates(config.Manuscripts, dockers)
 		return nil
 	})
 }
diff --git a/commands/version_manuscript.go b/cli/commands/version_manuscript.go
similarity index 100%
rename from commands/version_manuscript.go
rename to cli/commands/version_manuscript.go
diff --git a/go.mod b/cli/go.mod
similarity index 100%
rename from go.mod
rename to cli/go.mod
diff --git a/go.sum b/cli/go.sum
similarity index 100%
rename from go.sum
rename to cli/go.sum
diff --git a/main.go b/cli/main.go
similarity index 100%
rename from main.go
rename to cli/main.go
diff --git a/pkg/common_command.go b/cli/pkg/common_command.go
similarity index 100%
rename from pkg/common_command.go
rename to cli/pkg/common_command.go
diff --git a/pkg/docker_command.go b/cli/pkg/docker_command.go
similarity index 100%
rename from pkg/docker_command.go
rename to cli/pkg/docker_command.go
diff --git a/pkg/execute_step_with_loading.go b/cli/pkg/execute_step_with_loading.go
similarity index 100%
rename from pkg/execute_step_with_loading.go
rename to cli/pkg/execute_step_with_loading.go
diff --git a/pkg/manuscript_config.go b/cli/pkg/manuscript_config.go
similarity index 100%
rename from pkg/manuscript_config.go
rename to cli/pkg/manuscript_config.go
diff --git a/pkg/manuscript_parse.go b/cli/pkg/manuscript_parse.go
similarity index 100%
rename from pkg/manuscript_parse.go
rename to cli/pkg/manuscript_parse.go
diff --git a/pkg/manuscript_state.go b/cli/pkg/manuscript_state.go
similarity index 100%
rename from pkg/manuscript_state.go
rename to cli/pkg/manuscript_state.go
diff --git a/static/docker_compose_template.go b/cli/static/docker_compose_template.go
similarity index 100%
rename from static/docker_compose_template.go
rename to cli/static/docker_compose_template.go
diff --git a/static/manuscript_template.go b/cli/static/manuscript_template.go
similarity index 100%
rename from static/manuscript_template.go
rename to cli/static/manuscript_template.go