diff --git a/integration_test.go b/integration_test.go
index 75b0652e..bb1a04c1 100644
--- a/integration_test.go
+++ b/integration_test.go
@@ -2,6 +2,7 @@ package main
 
 import (
 	"bytes"
+	"fmt"
 	"os"
 	"os/exec"
 	"path/filepath"
@@ -1145,3 +1146,85 @@ Please fix issue number ${1} with priority ${2}.
 		t.Errorf("positional arguments not substituted in content. Output:\n%s", output)
 	}
 }
+
+func TestManifestFile(t *testing.T) {
+	// Create main project directory
+	mainDir := t.TempDir()
+	mainRulesDir := filepath.Join(mainDir, ".agents", "rules")
+	mainTasksDir := filepath.Join(mainDir, ".agents", "tasks")
+
+	if err := os.MkdirAll(mainRulesDir, 0o755); err != nil {
+		t.Fatalf("failed to create main rules dir: %v", err)
+	}
+	if err := os.MkdirAll(mainTasksDir, 0o755); err != nil {
+		t.Fatalf("failed to create main tasks dir: %v", err)
+	}
+
+	// Create a task file in the main directory
+	taskFile := filepath.Join(mainTasksDir, "test-task.md")
+	taskContent := `---
+task_name: test-task
+---
+# Test Task
+
+This is a test task.
+`
+	if err := os.WriteFile(taskFile, []byte(taskContent), 0o644); err != nil {
+		t.Fatalf("failed to write task file: %v", err)
+	}
+
+	// Create a rule file in the main directory (should be included)
+	mainRuleFile := filepath.Join(mainRulesDir, "main-rule.md")
+	mainRuleContent := `---
+---
+# Main Rule
+
+This rule is in the main project.
+`
+	if err := os.WriteFile(mainRuleFile, []byte(mainRuleContent), 0o644); err != nil {
+		t.Fatalf("failed to write main rule file: %v", err)
+	}
+
+	// Create a remote directory with rules
+	remoteDir := t.TempDir()
+	remoteRulesDir := filepath.Join(remoteDir, ".agents", "rules")
+	if err := os.MkdirAll(remoteRulesDir, 0o755); err != nil {
+		t.Fatalf("failed to create remote rules dir: %v", err)
+	}
+
+	remoteRuleFile := filepath.Join(remoteRulesDir, "remote-rule.md")
+	remoteRuleContent := `---
+---
+# Remote Rule
+
+This rule is from a remote directory.
+`
+	if err := os.WriteFile(remoteRuleFile, []byte(remoteRuleContent), 0o644); err != nil {
+		t.Fatalf("failed to write remote rule file: %v", err)
+	}
+
+	// Create a manifest file that references the remote directory
+	manifestFile := filepath.Join(t.TempDir(), "manifest.txt")
+	manifestContent := fmt.Sprintf("file://%s\n", remoteDir)
+	if err := os.WriteFile(manifestFile, []byte(manifestContent), 0o644); err != nil {
+		t.Fatalf("failed to write manifest file: %v", err)
+	}
+
+	// Run the tool with the manifest file
+	output := runTool(t, "-C", mainDir, "-m", "file://"+manifestFile, "/test-task")
+
+	// Check that the main rule is included
+	if !strings.Contains(output, "# Main Rule") {
+		t.Errorf("main rule not found in stdout. Output:\n%s", output)
+	}
+
+	// Check that the remote rule from the manifest is included
+	if !strings.Contains(output, "# Remote Rule") {
+		t.Errorf("remote rule from manifest not found in stdout. Output:\n%s", output)
+	}
+
+	// Check that the task is included
+	if !strings.Contains(output, "# Test Task") {
+		t.Errorf("task not found in stdout. Output:\n%s", output)
+	}
+}
diff --git a/pkg/codingcontext/context.go b/pkg/codingcontext/context.go
index c0365fa9..f585d529 100644
--- a/pkg/codingcontext/context.go
+++ b/pkg/codingcontext/context.go
@@ -115,6 +115,14 @@ func (cc *Context) expandParams(content string) string {
 // - A free-text prompt (used directly as task content)
 // - A prompt containing a slash command (e.g., "/fix-bug 123") which triggers task lookup
 func (cc *Context) Run(ctx context.Context, taskPrompt string) (*Result, error) {
+	// Parse manifest file first to get additional search paths
+	manifestPaths, err := cc.parseManifestFile(ctx)
+	if err != nil {
+		return nil, fmt.Errorf("failed to parse manifest file: %w", err)
+	}
+	cc.searchPaths = append(cc.searchPaths, manifestPaths...)
+
+	// Download all remote directories (including those from manifest)
 	if err := cc.downloadRemoteDirectories(ctx); err != nil {
 		return nil, fmt.Errorf("failed to download remote directories: %w", err)
 	}
@@ -130,12 +138,6 @@ func (cc *Context) Run(ctx context.Context, taskPrompt string) (*Result, error)
 		return nil, fmt.Errorf("failed to get user home directory: %w", err)
 	}
 
-	searchPaths, err := cc.parseManifestFile(ctx)
-	if err != nil {
-		return nil, fmt.Errorf("failed to parse manifest file: %w", err)
-	}
-	cc.searchPaths = append(cc.searchPaths, searchPaths...)
-
 	// Expand parameters in taskPrompt to allow slash commands in parameters
 	expandedTaskPrompt := cc.expandParams(taskPrompt)
 
@@ -226,8 +228,9 @@ func (cc *Context) parseManifestFile(ctx context.Context) ([]string, error) {
 
 	manifestFile := downloadDir(cc.manifestURL)
 
-	// Download the manifest file using go-getter
-	if _, err := getter.Get(ctx, manifestFile, cc.manifestURL); err != nil {
+	// Download the manifest file using go-getter's GetFile function
+	// GetFile is specifically for downloading single files (not directories)
+	if _, err := getter.GetFile(ctx, manifestFile, cc.manifestURL); err != nil {
 		return nil, fmt.Errorf("failed to download manifest file %s: %w", cc.manifestURL, err)
 	}
 	defer os.RemoveAll(manifestFile)