diff --git a/internal/cli/cli.go b/internal/cli/cli.go
index 5ae5eaa6f4..3f0213328f 100644
--- a/internal/cli/cli.go
+++ b/internal/cli/cli.go
@@ -21,6 +21,7 @@ import (
 	"encoding/json"
 	"errors"
 	"fmt"
+	"io"
 	"os"
 	//"os/signal"
 	"path/filepath"
@@ -177,7 +178,22 @@ func ParseArgs(args []string) (*CommandLineConfig, error) {
 		for i := 0; i < len(args); i++ {
 			arg := args[i]
 
-			// If we've found the command, collect remaining args as subcommand args
+			// Handle known global flags (already parsed in first pass).
+			// Intercept here regardless of position so they are never
+			// mistaken for command args or unknown flags downstream.
+			switch arg {
+			case "-o", "--output":
+				if i+1 < len(args) {
+					i++
+				}
+				continue
+			case "-v", "--verbose", "--help", "-help":
+				continue
+			case "--admin", "-admin":
+				return nil, fmt.Errorf("unexpected parameter: --admin")
+			}
+
+			// If we've found the command, collect remaining args
 			if foundCommand {
 				commandArgs = append(commandArgs, arg)
 				continue
@@ -222,17 +238,6 @@ func ParseArgs(args []string) (*CommandLineConfig, error) {
 					}
 					i++
 				}
-			case "-o", "--output":
-				// Already handled above
-				if i+1 < len(args) {
-					i++
-				}
-				continue
-			case "-v", "--verbose", "--help", "-help":
-				// Already handled above
-				continue
-			case "--admin", "-admin":
-				return nil, fmt.Errorf("unexpected parameter: --admin")
 			default:
 				// Non-flag argument (command)
 				if !strings.HasPrefix(arg, "-") {
@@ -311,7 +316,22 @@ func ParseArgs(args []string) (*CommandLineConfig, error) {
 		for i := 0; i < len(args); i++ {
 			arg := args[i]
 
-			// If we've found the command, collect remaining args as subcommand args
+			// Handle known global flags regardless of position
+			switch arg {
+			case "-o", "--output":
+				if i+1 < len(args) {
+					i++
+				}
+				continue
+			case "-v", "--verbose", "--admin", "-admin", "--help", "-help":
+				continue
+			case "-t", "--token":
+				return nil, fmt.Errorf("token is invalid in admin mode")
+			case "-f", "--config":
+				return nil, fmt.Errorf("config is invalid in admin mode")
+			}
+
+			// If we've found the command, collect remaining args
 			if foundCommand {
 				commandArgs = append(commandArgs, arg)
 				continue
@@ -329,8 +349,6 @@ func ParseArgs(args []string) (*CommandLineConfig, error) {
 					AdminConfig.AdminPort = port
 					i++
 				}
-			case "-t", "--token":
-				return nil, fmt.Errorf("token is invalid in admin mode")
 			case "-u", "--user":
 				if i+1 < len(args) && !strings.HasPrefix(args[i+1], "-") {
 					AdminConfig.AdminName = &args[i+1]
@@ -341,17 +359,6 @@ func ParseArgs(args []string) (*CommandLineConfig, error) {
 					AdminConfig.AdminPassword = &args[i+1]
 					i++
 				}
-			case "-f", "--config":
-				return nil, fmt.Errorf("config is invalid in admin mode")
-			case "-o", "--output":
-				// Already handled above
-				if i+1 < len(args) {
-					i++
-				}
-				continue
-			case "-v", "--verbose", "--admin", "-admin", "--help", "-help":
-				// Already handled above
-				continue
 			default:
 				// Non-flag argument (command)
 				if !strings.HasPrefix(arg, "-") {
@@ -534,8 +541,9 @@ func NewCLIWithConfig(commandLineConfig *CommandLineConfig) (*CLI, error) {
 	line := liner.NewLiner()
 
 	cli := &CLI{
-		line:   line,
-		Config: commandLineConfig,
+		line:         line,
+		Config:       commandLineConfig,
+		outputFormat: commandLineConfig.OutputFormat,
 	}
 
 	if commandLineConfig.CLIMode == APIMode {
@@ -789,11 +797,50 @@ func (c *CLI) execute(input string) error {
 	}
 
 	// Filesystem mode: execute filesystem command
-	return c.executeFilesystem(input)
+	cmd := NewCommand("file_system_command")
+	cmd.Params["command"] = input
+	resp, ceErr := c.executeFilesystem(cmd)
+	if resp != nil {
+		resp.PrintOut()
+	}
+	return ceErr
 }
 
-// executeFilesystem executes a Filesystem command
-func (c *CLI) executeFilesystem(input string) error {
+// executeFilesystem executes a Filesystem command and returns a ResponseIf.
+func (c *CLI) executeFilesystem(cmd *Command) (ResponseIf, error) {
+	rawInput, _ := cmd.Params["command"].(string)
+
+	r, w, err := os.Pipe()
+	if err != nil {
+		return nil, fmt.Errorf("create stdout pipe: %w", err)
+	}
+	old := os.Stdout
+	os.Stdout = w
+	defer func() {
+		os.Stdout = old
+		_ = w.Close()
+		_ = r.Close()
+	}()
+
+	var buf strings.Builder
+	copyErrCh := make(chan error, 1)
+	go func() {
+		_, copyErr := io.Copy(&buf, r)
+		copyErrCh <- copyErr
+	}()
+
+	execErr := c.executeFilesystemInner(rawInput)
+	_ = w.Close() // signal EOF to reader goroutine
+	copyErr := <-copyErrCh
+	if copyErr != nil {
+		return nil, fmt.Errorf("capture filesystem output: %w", copyErr)
+	}
+	return &FileSystemResponse{Output: buf.String()}, execErr
+}
+
+// executeFilesystemInner executes a Filesystem command and writes output to stdout.
+// It is called by executeFilesystem which captures the stdout output.
+func (c *CLI) executeFilesystemInner(input string) error {
 	// Parse input into arguments
 	var args []string
 	if c.args != nil && len(c.args.CommandArgs) > 0 {
@@ -947,36 +994,6 @@ func (c *CLI) executeFilesystem(input string) error {
 		fileProv, _ := fileProvider.(*filesystem.FileProvider)
 		cmd := filesystem.NewUninstallSkillCommand(httpAdapter, skillProvider, fileProv)
 		return cmd.Execute(cmdArgs)
-	case "add-skill":
-		fmt.Println("⚠ Warning: 'add-skill' is deprecated. Use 'install-skill' instead.")
-		// Forward to install-skill
-		fileProvider, ok := c.ContextEngine.GetProvider("files").(*filesystem.FileProvider)
-		if !ok {
-			return fmt.Errorf("file provider not available")
-		}
-		skillProvider := c.ContextEngine.GetProvider("skills")
-		if skillProvider == nil {
-			return fmt.Errorf("skill provider not available")
-		}
-		httpAdapter := &httpClientAdapter{client: httpClient}
-		cmd := filesystem.NewInstallSkillCommand(httpAdapter, fileProvider, skillProvider)
-		return cmd.Execute(cmdArgs)
-	case "delete-skill":
-		fmt.Println("⚠ Warning: 'delete-skill' is deprecated. Use 'uninstall-skill' instead.")
-		// Forward to uninstall-skill
-		skillProvider := c.ContextEngine.GetProvider("skills")
-		if skillProvider == nil {
-			return fmt.Errorf("skill provider not available")
-		}
-		fileProvider := c.ContextEngine.GetProvider("files")
-		if fileProvider == nil {
-			return fmt.Errorf("file provider not available")
-		}
-		httpAdapter := &httpClientAdapter{client: httpClient}
-		fileProv, _ := fileProvider.(*filesystem.FileProvider)
-		cmd := filesystem.NewUninstallSkillCommand(httpAdapter, skillProvider, fileProv)
-		return cmd.Execute(cmdArgs)
-
 	default:
 		return fmt.Errorf("unknown filesystem command: %s", cmdType)
 	}
diff --git a/internal/cli/cli_http.go b/internal/cli/cli_http.go
index 03abbef220..6135a79a97 100644
--- a/internal/cli/cli_http.go
+++ b/internal/cli/cli_http.go
@@ -294,9 +294,8 @@ func (c *CLI) ExecuteUserCommand(cmd *Command) (ResponseIf, error) {
 		return c.DeleteAdminServer(cmd)
 	case "save_config_command":
 		return c.SaveServerConfig(cmd)
-	// ContextEngine commands
-	case "context_engine_command":
-		return nil, c.executeFilesystem(cmd.Params["command"].(string))
+	case "file_system_command":
+		return c.executeFilesystem(cmd)
 	default:
 		return nil, fmt.Errorf("command '%s' would be executed with API", cmd.Type)
 	}
diff --git a/internal/cli/context_parser.go b/internal/cli/context_parser.go
deleted file mode 100644
index 324ec39c07..0000000000
--- a/internal/cli/context_parser.go
+++ /dev/null
@@ -1,178 +0,0 @@
-//
-//  Copyright 2026 The InfiniFlow Authors. All Rights Reserved.
-//
-//  Licensed under the Apache License, Version 2.0 (the "License");
-//  you may not use this file except in compliance with the License.
-//  You may obtain a copy of the License at
-//
-//      http://www.apache.org/licenses/LICENSE-2.0
-//
-//  Unless required by applicable law or agreed to in writing, software
-//  distributed under the License is distributed on an "AS IS" BASIS,
-//  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-//  See the License for the specific language governing permissions and
-//  limitations under the License.
-//
-
-package cli
-
-import (
-	"fmt"
-	"strings"
-)
-
-func (p *Parser) parseContextListCommand() (*Command, error) {
-	p.nextToken() // consume LS
-
-	cmd := NewCommand("ce_ls")
-
-	if p.curToken.Type == TokenEOF {
-		cmd.Params["path"] = "."
-		return cmd, nil
-	}
-
-	for p.curToken.Type != TokenEOF {
-		if p.curToken.Type == TokenDash {
-			p.nextToken() // skip dash
-			if p.curToken.Type != TokenIdentifier {
-				return nil, fmt.Errorf("expect identifier")
-			}
-			if cmd.Params["parameter"] == nil {
-				cmd.Params["parameter"] = p.curToken.Value
-			} else {
-				cmd.Params["parameter"] = fmt.Sprintf("%s%s", cmd.Params["parameter"], p.curToken.Value)
-			}
-			p.nextToken() // skip parameter
-		} else if p.curToken.Type == TokenIdentifier {
-			if cmd.Params["path"] == nil {
-				cmd.Params["path"] = p.curToken.Value
-			} else {
-				err := fmt.Errorf("ls: cannot access '%s': No such file or directory", p.curToken.Value)
-				return nil, err
-			}
-			p.nextToken() // skip path
-		} else {
-			return nil, fmt.Errorf("syntax error")
-		}
-	}
-
-	return cmd, nil
-}
-
-func (p *Parser) parseContextCatCommand() (*Command, error) {
-	p.nextToken() // consume CAT
-
-	if p.curToken.Type == TokenEOF {
-		return nil, fmt.Errorf("expect a filename")
-	}
-
-	if p.curToken.Type != TokenIdentifier && p.curToken.Type != TokenQuotedString {
-		return nil, fmt.Errorf("expect a filename")
-	}
-
-	cmd := NewCommand("ce_cat")
-	if p.curToken.Type == TokenIdentifier {
-		for p.curToken.Type != TokenEOF {
-			if p.curToken.Type != TokenIdentifier {
-				return nil, fmt.Errorf("expect a identifier")
-			}
-
-			if cmd.Params["filename"] == nil {
-				cmd.Params["filename"] = p.curToken.Value
-			} else {
-				cmd.Params["filename"] = fmt.Sprintf("%s/%s", cmd.Params["filename"], p.curToken.Value)
-			}
-			p.nextToken()
-			if p.curToken.Type == TokenEOF {
-				break
-			}
-			if p.curToken.Type != TokenSlash {
-				return nil, fmt.Errorf("expect a slash")
-			}
-			p.nextToken()
-			if p.curToken.Type == TokenEOF {
-				return nil, fmt.Errorf("error format")
-			}
-		}
-
-	} else if p.curToken.Type == TokenQuotedString {
-		var err error
-		cmd.Params["filename"], err = p.parseQuotedString()
-		if err != nil {
-			return nil, err
-		}
-	}
-	p.nextToken()
-
-	if p.curToken.Type != TokenEOF {
-		return nil, fmt.Errorf("syntax error")
-	}
-
-	return cmd, nil
-}
-
-func (p *Parser) parseContextSearchCommand() (*Command, error) {
-	p.nextToken() // consume SEARCH
-
-	cmd := NewCommand("ce_search")
-
-	for p.curToken.Type != TokenEOF {
-		if p.curToken.Type == TokenDash {
-			p.nextToken() // skip dash
-			if p.curToken.Type != TokenIdentifier {
-				return nil, fmt.Errorf("expect identifier")
-			}
-
-			if strings.ToLower(p.curToken.Value) == "n" {
-				p.nextToken()
-				var err error
-				if p.curToken.Type != TokenInteger {
-					return nil, fmt.Errorf("expect number")
-				}
-				cmd.Params["number"], err = p.parseNumber()
-				if err != nil {
-					return nil, err
-				}
-				p.nextToken()
-				continue
-			}
-
-			if strings.ToLower(p.curToken.Value) == "t" {
-				p.nextToken()
-				var err error
-				if p.curToken.Type != TokenInteger {
-					return nil, fmt.Errorf("expect number")
-				}
-				cmd.Params["threshold"], err = p.parseFloat()
-				if err != nil {
-					return nil, err
-				}
-				p.nextToken()
-				continue
-			}
-
-			return nil, fmt.Errorf("unknow parameter: %s", p.curToken.Value)
-		} else if p.curToken.Type == TokenIdentifier {
-			if cmd.Params["path"] == nil {
-				cmd.Params["path"] = p.curToken.Value
-			} else {
-				cmd.Params["path"] = fmt.Sprintf("%s %s", cmd.Params["path"], p.curToken.Value)
-			}
-			p.nextToken() // skip path
-		} else if p.curToken.Type == TokenQuotedString {
-			if cmd.Params["query"] == nil {
-				var err error
-				cmd.Params["query"], err = p.parseQuotedString()
-				if err != nil {
-					return nil, err
-				}
-				p.nextToken()
-			} else {
-				return nil, fmt.Errorf("Query phrase exists")
-			}
-		}
-		return nil, fmt.Errorf("syntax error")
-	}
-
-	return cmd, nil
-}
diff --git a/internal/cli/parser.go b/internal/cli/parser.go
index 4c2fbcb7e1..04253b051a 100644
--- a/internal/cli/parser.go
+++ b/internal/cli/parser.go
@@ -227,7 +227,7 @@ func (p *Parser) parseUserCommand() (*Command, error) {
 
 	case TokenLS, TokenCat, TokenSearch:
 		// For context engine
-		return p.parseContextEngineCommand()
+		return p.parseFileSystemCommand()
 	default:
 		return nil, fmt.Errorf("unknown command: %s", p.curToken.Value)
 	}
@@ -390,241 +390,13 @@ func tokenTypeToString(t int) string {
 	return fmt.Sprintf("token(%d)", t)
 }
 
-func (p *Parser) parseContextEngineCommand() (*Command, error) {
+func (p *Parser) parseFileSystemCommand() (*Command, error) {
 	p.nextToken() // consume COMMAND
 
-	cmd := NewCommand("context_engine_command")
+	cmd := NewCommand("file_system_command")
 	cmd.Params["command"] = p.original
 
 	return cmd, nil
 }
 
-// parseCEListCommand parses the ls command
-// Syntax: ls [path] or ls datasets
-func (p *Parser) parseCEListCommand() (*Command, error) {
-	p.nextToken() // consume LS/LIST
 
-	cmd := NewCommand("ce_ls")
-
-	// Check if there's a path argument
-	// Also accept TokenDatasets since "datasets" is a keyword but can be a path
-	if p.curToken.Type == TokenIdentifier || p.curToken.Type == TokenQuotedString ||
-		p.curToken.Type == TokenDatasets {
-		path := p.curToken.Value
-		// Remove quotes if present
-		if p.curToken.Type == TokenQuotedString {
-			path = strings.Trim(path, "\"'")
-		}
-		p.nextToken()
-
-		// Handle path components separated by slashes (e.g., "skills/hub1")
-		for p.curToken.Type == TokenSlash {
-			p.nextToken() // consume slash
-			if p.curToken.Type == TokenIdentifier || p.curToken.Type == TokenDatasets ||
-				p.curToken.Type == TokenAgents || p.curToken.Type == TokenChats {
-				path = path + "/" + p.curToken.Value
-				p.nextToken()
-			} else if p.curToken.Type == TokenNumber {
-				// Handle version numbers like 1.0.0 (parsed as number . number . number)
-				// OR filenames starting with numbers like 3_list_compressors.pdf
-				numberPart := p.curToken.Value
-				p.nextToken()
-				// Continue reading .number parts (version number format)
-				if p.curToken.Type == TokenIllegal && p.curToken.Value == "." {
-					versionPart := numberPart
-					for p.curToken.Type == TokenIllegal && p.curToken.Value == "." {
-						p.nextToken() // consume .
-						if p.curToken.Type == TokenNumber {
-							versionPart = versionPart + "." + p.curToken.Value
-							p.nextToken()
-						} else {
-							break
-						}
-					}
-					path = path + "/" + versionPart
-				} else if p.curToken.Type == TokenIdentifier {
-					// Filename starting with number: 3_list_compressors.pdf
-					path = path + "/" + numberPart + p.curToken.Value
-					p.nextToken()
-				} else {
-					// Just a number
-					path = path + "/" + numberPart
-				}
-			} else {
-				// Trailing slash, just append it
-				path = path + "/"
-				break
-			}
-		}
-
-		cmd.Params["path"] = path
-	} else {
-		// Default to "datasets" root
-		cmd.Params["path"] = "datasets"
-	}
-
-	// Optional semicolon
-	if p.curToken.Type == TokenSemicolon {
-		p.nextToken()
-	}
-
-	return cmd, nil
-}
-
-// parseCECatCommand parses the cat command
-// Syntax: cat <path>
-func (p *Parser) parseCECatCommand() (*Command, error) {
-	p.nextToken() // consume CAT
-
-	cmd := NewCommand("ce_cat")
-
-	if p.curToken.Type != TokenIdentifier && p.curToken.Type != TokenQuotedString {
-		return nil, fmt.Errorf("expected path after CAT")
-	}
-
-	path := p.curToken.Value
-	if p.curToken.Type == TokenQuotedString {
-		path = strings.Trim(path, "\"'")
-	}
-	p.nextToken()
-
-	// Handle path components separated by slashes (e.g., "skills/hub1/skill/README.md")
-	for p.curToken.Type == TokenSlash {
-		p.nextToken() // consume slash
-		if p.curToken.Type == TokenIdentifier || p.curToken.Type == TokenAgents ||
-			p.curToken.Type == TokenChats || p.curToken.Type == TokenDatasets {
-			path = path + "/" + p.curToken.Value
-			p.nextToken()
-		} else if p.curToken.Type == TokenNumber {
-			// Handle version numbers like 1.0.0 (parsed as number . number . number)
-			// OR filenames starting with numbers like 3_list_compressors.pdf
-			numberPart := p.curToken.Value
-			p.nextToken()
-			// Continue reading .number parts (version number format)
-			if p.curToken.Type == TokenIllegal && p.curToken.Value == "." {
-				versionPart := numberPart
-				for p.curToken.Type == TokenIllegal && p.curToken.Value == "." {
-					p.nextToken() // consume .
-					if p.curToken.Type == TokenNumber {
-						versionPart = versionPart + "." + p.curToken.Value
-						p.nextToken()
-					} else {
-						break
-					}
-				}
-				path = path + "/" + versionPart
-			} else if p.curToken.Type == TokenIdentifier {
-				// Filename starting with number: 3_list_compressors.pdf
-				path = path + "/" + numberPart + p.curToken.Value
-				p.nextToken()
-			} else {
-				// Just a number
-				path = path + "/" + numberPart
-			}
-		} else if p.curToken.Type == TokenQuotedString {
-			path = path + "/" + strings.Trim(p.curToken.Value, "\"'")
-			p.nextToken()
-		} else {
-			// Trailing slash, just append it
-			path = path + "/"
-			break
-		}
-	}
-
-	cmd.Params["path"] = path
-
-	// Optional semicolon
-	if p.curToken.Type == TokenSemicolon {
-		p.nextToken()
-	}
-
-	return cmd, nil
-}
-
-// parseCESearchCommand parses the search command
-// Syntax: search <query> or search <query> in <path>
-func (p *Parser) parseCESearchCommand() (*Command, error) {
-	p.nextToken() // consume SEARCH
-
-	cmd := NewCommand("ce_search")
-
-	if p.curToken.Type != TokenIdentifier && p.curToken.Type != TokenQuotedString {
-		return nil, fmt.Errorf("expected query after SEARCH")
-	}
-
-	query := p.curToken.Value
-	if p.curToken.Type == TokenQuotedString {
-		query = strings.Trim(query, "\"'")
-	}
-	cmd.Params["query"] = query
-	p.nextToken()
-
-	// Check for optional "in <path>" clause
-	if p.curToken.Type == TokenIdentifier && strings.ToUpper(p.curToken.Value) == "IN" {
-		p.nextToken() // consume IN
-
-		if p.curToken.Type != TokenIdentifier && p.curToken.Type != TokenQuotedString {
-			return nil, fmt.Errorf("expected path after IN")
-		}
-
-		path := p.curToken.Value
-		if p.curToken.Type == TokenQuotedString {
-			path = strings.Trim(path, "\"'")
-		}
-		p.nextToken()
-
-		// Handle path components separated by slashes (e.g., "skills/hub1")
-		for p.curToken.Type == TokenSlash {
-			p.nextToken() // consume slash
-			if p.curToken.Type == TokenIdentifier || p.curToken.Type == TokenAgents ||
-				p.curToken.Type == TokenChats || p.curToken.Type == TokenDatasets {
-				path = path + "/" + p.curToken.Value
-				p.nextToken()
-			} else if p.curToken.Type == TokenNumber {
-				// Handle version numbers like 1.0.0 (parsed as number . number . number)
-				// OR filenames starting with numbers like 3_list_compressors.pdf
-				numberPart := p.curToken.Value
-				p.nextToken()
-				// Continue reading .number parts (version number format)
-				if p.curToken.Type == TokenIllegal && p.curToken.Value == "." {
-					versionPart := numberPart
-					for p.curToken.Type == TokenIllegal && p.curToken.Value == "." {
-						p.nextToken() // consume .
-						if p.curToken.Type == TokenNumber {
-							versionPart = versionPart + "." + p.curToken.Value
-							p.nextToken()
-						} else {
-							break
-						}
-					}
-					path = path + "/" + versionPart
-				} else if p.curToken.Type == TokenIdentifier {
-					// Filename starting with number: 3_list_compressors.pdf
-					path = path + "/" + numberPart + p.curToken.Value
-					p.nextToken()
-				} else {
-					// Just a number
-					path = path + "/" + numberPart
-				}
-			} else if p.curToken.Type == TokenQuotedString {
-				path = path + "/" + strings.Trim(p.curToken.Value, "\"'")
-				p.nextToken()
-			} else {
-				// Trailing slash, just append it
-				path = path + "/"
-				break
-			}
-		}
-
-		cmd.Params["path"] = path
-	} else {
-		cmd.Params["path"] = "."
-	}
-
-	// Optional semicolon
-	if p.curToken.Type == TokenSemicolon {
-		p.nextToken()
-	}
-
-	return cmd, nil
-}
diff --git a/internal/cli/response.go b/internal/cli/response.go
index 7bf7150b6d..054ceb4430 100644
--- a/internal/cli/response.go
+++ b/internal/cli/response.go
@@ -529,69 +529,16 @@ func (r *TaskResponse) PrintOut() {
 	}
 }
 
-// ==================== ContextEngine Commands ====================
-
-// ContextListResponse represents the response for ls command
-type ContextListResponse struct {
-	Code         int                      `json:"code"`
-	Data         []map[string]interface{} `json:"data"`
-	Message      string                   `json:"message"`
+// FileSystemResponse wraps the raw text output from executeFilesystem().
+type FileSystemResponse struct {
+	Output       string
 	Duration     float64
 	OutputFormat OutputFormat
 }
 
-func (r *ContextListResponse) Type() string                        { return "ce_ls" }
-func (r *ContextListResponse) TimeCost() float64                   { return r.Duration }
-func (r *ContextListResponse) SetOutputFormat(format OutputFormat) { r.OutputFormat = format }
-func (r *ContextListResponse) PrintOut() {
-	if r.Code == 0 {
-		PrintTableSimpleByFormat(r.Data, r.OutputFormat)
-	} else {
-		fmt.Println("ERROR")
-		fmt.Printf("%d, %s\n", r.Code, r.Message)
-	}
-}
-
-// ContextSearchResponse represents the response for search command
-type ContextSearchResponse struct {
-	Code         int                      `json:"code"`
-	Data         []map[string]interface{} `json:"data"`
-	Total        int                      `json:"total"`
-	Message      string                   `json:"message"`
-	Duration     float64
-	OutputFormat OutputFormat
-}
-
-func (r *ContextSearchResponse) Type() string                        { return "ce_search" }
-func (r *ContextSearchResponse) TimeCost() float64                   { return r.Duration }
-func (r *ContextSearchResponse) SetOutputFormat(format OutputFormat) { r.OutputFormat = format }
-func (r *ContextSearchResponse) PrintOut() {
-	if r.Code == 0 {
-		fmt.Printf("Found %d results:\n", r.Total)
-		PrintTableSimpleByFormat(r.Data, r.OutputFormat)
-	} else {
-		fmt.Println("ERROR")
-		fmt.Printf("%d, %s\n", r.Code, r.Message)
-	}
-}
-
-// ContextCatResponse represents the response for cat command
-type ContextCatResponse struct {
-	Code         int    `json:"code"`
-	Content      string `json:"content"`
-	Message      string `json:"message"`
-	Duration     float64
-	OutputFormat OutputFormat
-}
-
-func (r *ContextCatResponse) Type() string                        { return "ce_cat" }
-func (r *ContextCatResponse) TimeCost() float64                   { return r.Duration }
-func (r *ContextCatResponse) SetOutputFormat(format OutputFormat) { r.OutputFormat = format }
-func (r *ContextCatResponse) PrintOut() {
-	if r.Code == 0 {
-		fmt.Println(r.Content)
-	} else {
-		fmt.Println("ERROR")
-		fmt.Printf("%d, %s\n", r.Code, r.Message)
-	}
+func (r *FileSystemResponse) Type() string                        { return "filesystem" }
+func (r *FileSystemResponse) TimeCost() float64                   { return r.Duration }
+func (r *FileSystemResponse) SetOutputFormat(format OutputFormat) { r.OutputFormat = format }
+func (r *FileSystemResponse) PrintOut() {
+	fmt.Print(r.Output)
 }
diff --git a/internal/cli/user_command.go b/internal/cli/user_command.go
index ccf8611c39..b783ebc6d5 100644
--- a/internal/cli/user_command.go
+++ b/internal/cli/user_command.go
@@ -18,7 +18,6 @@ package cli
 
 import (
 	"bufio"
-	"context"
 	"encoding/base64"
 	"encoding/json"
 	"errors"
@@ -29,7 +28,6 @@ import (
 	"os"
 	"os/exec"
 	"path/filepath"
-	ce "ragflow/internal/cli/filesystem"
 	"strings"
 	"time"
 )
@@ -2736,113 +2734,6 @@ func (c *CLI) AddCustomModel(cmd *Command) (ResponseIf, error) {
 
 }
 
-// Context related commands
-
-// CECat handles the cat command - shows content using Context Engine
-func (c *CLI) CECat(cmd *Command) (ResponseIf, error) {
-	if c.APIServerClientMap[c.Config.APIClientConfig.CurrentAPIServer].APIToken == nil && c.APIServerClientMap[c.Config.APIClientConfig.CurrentAPIServer].LoginToken == nil {
-		return nil, fmt.Errorf("API token not set. Please login first")
-	}
-	if c.Config.CLIMode != APIMode {
-		return nil, fmt.Errorf("this command is only allowed in USER mode")
-	}
-
-	path, ok := cmd.Params["path"].(string)
-	if !ok {
-		return nil, fmt.Errorf("fail to convert 'path' to string")
-	}
-
-	// Execute cat command through Filesystem Engine
-	ctx := context.Background()
-	content, err := c.ContextEngine.Cat(ctx, path)
-	if err != nil {
-		return nil, err
-	}
-
-	// Convert to response
-	var response ContextCatResponse
-	response.OutputFormat = c.outputFormat
-	response.Code = 0
-	response.Content = string(content)
-
-	return &response, nil
-}
-
-// CEList handles the ls command - lists nodes using Context Engine
-func (c *CLI) CEList(cmd *Command) (ResponseIf, error) {
-	// Get path from command params, default to "datasets"
-	path, _ := cmd.Params["path"].(string)
-	if path == "" {
-		path = "datasets"
-	}
-
-	// Parse options
-	opts := &ce.ListOptions{}
-	if recursive, ok := cmd.Params["recursive"].(bool); ok {
-		opts.Recursive = recursive
-	}
-	if limit, ok := cmd.Params["limit"].(int); ok {
-		opts.Limit = limit
-	}
-	if offset, ok := cmd.Params["offset"].(int); ok {
-		opts.Offset = offset
-	}
-
-	// Execute list command through Filesystem Engine
-	ctx := context.Background()
-	result, err := c.ContextEngine.List(ctx, path, opts)
-	if err != nil {
-		return nil, err
-	}
-
-	// Convert to response
-	var response ContextListResponse
-	response.OutputFormat = c.outputFormat
-	response.Code = 0
-	response.Data = ce.FormatNodes(result.Nodes, string(c.outputFormat))
-
-	return &response, nil
-}
-
-// CESearch handles the search command using Context Engine
-func (c *CLI) CESearch(cmd *Command) (ResponseIf, error) {
-	// Get path and query from command params
-	path, _ := cmd.Params["path"].(string)
-	if path == "" {
-		path = "datasets"
-	}
-	query, _ := cmd.Params["query"].(string)
-
-	// Parse options
-	opts := &ce.SearchOptions{
-		Query: query,
-	}
-	if limit, ok := cmd.Params["limit"].(int); ok {
-		opts.Limit = limit
-	}
-	if offset, ok := cmd.Params["offset"].(int); ok {
-		opts.Offset = offset
-	}
-	if recursive, ok := cmd.Params["recursive"].(bool); ok {
-		opts.Recursive = recursive
-	}
-
-	// Execute search command through Filesystem Engine
-	ctx := context.Background()
-	result, err := c.ContextEngine.Search(ctx, path, opts)
-	if err != nil {
-		return nil, err
-	}
-
-	// Convert to response
-	var response ContextSearchResponse
-	response.OutputFormat = c.outputFormat
-	response.Code = 0
-	response.Total = result.Total
-	response.Data = ce.FormatNodes(result.Nodes, string(c.outputFormat))
-
-	return &response, nil
-}
 
 // InsertChunksFromFile inserts chunks from a JSON file
 func (c *CLI) InsertChunksFromFile(cmd *Command) (ResponseIf, error) {