diff --git a/cmd/compile.go b/cmd/compile.go
new file mode 100644
index 0000000..62308e9
--- /dev/null
+++ b/cmd/compile.go
@@ -0,0 +1,63 @@
+package cmd
+
+import (
+	"fmt"
+	"os"
+	"strings"
+
+	"github.com/Snider/Borg/pkg/matrix"
+	"github.com/spf13/cobra"
+)
+
+var borgfile string
+var output string
+
+var compileCmd = &cobra.Command{
+	Use:   "compile",
+	Short: "Compile a Borgfile into a Terminal Isolation Matrix.",
+	RunE: func(cmd *cobra.Command, args []string) error {
+		content, err := os.ReadFile(borgfile)
+		if err != nil {
+			return err
+		}
+
+		m, err := matrix.New()
+		if err != nil {
+			return err
+		}
+
+		lines := strings.Split(string(content), "\n")
+		for _, line := range lines {
+			parts := strings.Fields(line)
+			if len(parts) == 0 {
+				continue
+			}
+			switch parts[0] {
+			case "ADD":
+				if len(parts) != 3 {
+					return fmt.Errorf("invalid ADD instruction: %s", line)
+				}
+				src := parts[1]
+				dest := parts[2]
+				data, err := os.ReadFile(src)
+				if err != nil {
+					return err
+				}
+				m.RootFS.AddData(dest, data)
+			}
+		}
+
+		tarball, err := m.ToTar()
+		if err != nil {
+			return err
+		}
+
+		return os.WriteFile(output, tarball, 0644)
+	},
+}
+
+func init() {
+	RootCmd.AddCommand(compileCmd)
+	compileCmd.Flags().StringVarP(&borgfile, "file", "f", "Borgfile", "Path to the Borgfile.")
+	compileCmd.Flags().StringVarP(&output, "output", "o", "a.matrix", "Path to the output matrix file.")
+}
diff --git a/cmd/compile_test.go b/cmd/compile_test.go
new file mode 100644
index 0000000..42c8a93
--- /dev/null
+++ b/cmd/compile_test.go
@@ -0,0 +1,77 @@
+package cmd
+
+import (
+	"archive/tar"
+	"io"
+	"os"
+	"path/filepath"
+	"testing"
+)
+
+func TestCompileCmd_Good(t *testing.T) {
+	tempDir := t.TempDir()
+	borgfilePath := filepath.Join(tempDir, "Borgfile")
+	outputMatrixPath := filepath.Join(tempDir, "test.matrix")
+	fileToAddPath := filepath.Join(tempDir, "test.txt")
+
+	// Create a dummy file to add to the matrix.
+	err := os.WriteFile(fileToAddPath, []byte("hello world"), 0644)
+	if err != nil {
+		t.Fatalf("failed to create test file: %v", err)
+	}
+
+	// Create a dummy Borgfile.
+	borgfileContent := "ADD " + fileToAddPath + " /test.txt"
+	err = os.WriteFile(borgfilePath, []byte(borgfileContent), 0644)
+	if err != nil {
+		t.Fatalf("failed to create Borgfile: %v", err)
+	}
+
+	// Run the compile command.
+	rootCmd := NewRootCmd()
+	rootCmd.AddCommand(compileCmd)
+	_, err = executeCommand(rootCmd, "compile", "-f", borgfilePath, "-o", outputMatrixPath)
+	if err != nil {
+		t.Fatalf("compile command failed: %v", err)
+	}
+
+	// Verify the output matrix file.
+	matrixFile, err := os.Open(outputMatrixPath)
+	if err != nil {
+		t.Fatalf("failed to open output matrix file: %v", err)
+	}
+	defer matrixFile.Close()
+
+	tr := tar.NewReader(matrixFile)
+	foundConfig := false
+	foundRootFS := false
+	foundTestFile := false
+	for {
+		header, err := tr.Next()
+		if err == io.EOF {
+			break
+		}
+		if err != nil {
+			t.Fatalf("failed to read tar header: %v", err)
+		}
+
+		switch header.Name {
+		case "config.json":
+			foundConfig = true
+		case "rootfs/":
+			foundRootFS = true
+		case "rootfs/test.txt":
+			foundTestFile = true
+		}
+	}
+
+	if !foundConfig {
+		t.Error("config.json not found in matrix")
+	}
+	if !foundRootFS {
+		t.Error("rootfs/ not found in matrix")
+	}
+	if !foundTestFile {
+		t.Error("rootfs/test.txt not found in matrix")
+	}
+}
diff --git a/cmd/exec.go b/cmd/exec.go
new file mode 100644
index 0000000..91fd126
--- /dev/null
+++ b/cmd/exec.go
@@ -0,0 +1,5 @@
+package cmd
+
+import "os/exec"
+
+var execCommand = exec.Command
diff --git a/cmd/main_test.go b/cmd/main_test.go
new file mode 100644
index 0000000..70aa8fa
--- /dev/null
+++ b/cmd/main_test.go
@@ -0,0 +1,25 @@
+package cmd
+
+import (
+	"bytes"
+
+	"github.com/spf13/cobra"
+)
+
+// executeCommand is a helper function to execute a cobra command and return the output.
+func executeCommand(root *cobra.Command, args ...string) (string, error) {
+	_, output, err := executeCommandC(root, args...)
+	return output, err
+}
+
+// executeCommandC is a helper function to execute a cobra command and return the output.
+func executeCommandC(root *cobra.Command, args ...string) (*cobra.Command, string, error) {
+	buf := new(bytes.Buffer)
+	root.SetOut(buf)
+	root.SetErr(buf)
+	root.SetArgs(args)
+
+	c, err := root.ExecuteC()
+
+	return c, buf.String(), err
+}
diff --git a/cmd/root_test.go b/cmd/root_test.go
index 34e5b4a..e632e29 100644
--- a/cmd/root_test.go
+++ b/cmd/root_test.go
@@ -1,7 +1,6 @@
 package cmd
 
 import (
-	"bytes"
 	"io"
 	"log/slog"
 	"testing"
@@ -16,15 +15,6 @@ func TestExecute(t *testing.T) {
 	}
 }
 
-func executeCommand(cmd *cobra.Command, args ...string) (string, error) {
-	buf := new(bytes.Buffer)
-	cmd.SetOut(buf)
-	cmd.SetErr(buf)
-	cmd.SetArgs(args)
-
-	err := cmd.Execute()
-	return buf.String(), err
-}
 
 func Test_NewRootCmd(t *testing.T) {
 	if NewRootCmd() == nil {
diff --git a/cmd/run.go b/cmd/run.go
new file mode 100644
index 0000000..2044826
--- /dev/null
+++ b/cmd/run.go
@@ -0,0 +1,73 @@
+package cmd
+
+import (
+	"archive/tar"
+	"io"
+	"os"
+	"path/filepath"
+
+	"github.com/spf13/cobra"
+)
+
+var runCmd = &cobra.Command{
+	Use:   "run [matrix file]",
+	Short: "Run a Terminal Isolation Matrix.",
+	Args:  cobra.ExactArgs(1),
+	RunE: func(cmd *cobra.Command, args []string) error {
+		matrixFile := args[0]
+
+		// Create a temporary directory to unpack the matrix file.
+		tempDir, err := os.MkdirTemp("", "borg-run-*")
+		if err != nil {
+			return err
+		}
+		defer os.RemoveAll(tempDir)
+
+		// Unpack the matrix file.
+		file, err := os.Open(matrixFile)
+		if err != nil {
+			return err
+		}
+		defer file.Close()
+
+		tr := tar.NewReader(file)
+		for {
+			header, err := tr.Next()
+			if err == io.EOF {
+				break
+			}
+			if err != nil {
+				return err
+			}
+
+			path := filepath.Join(tempDir, header.Name)
+			if header.Typeflag == tar.TypeDir {
+				if err := os.MkdirAll(path, 0755); err != nil {
+					return err
+				}
+				continue
+			}
+
+			outFile, err := os.Create(path)
+			if err != nil {
+				return err
+			}
+			defer outFile.Close()
+			if _, err := io.Copy(outFile, tr); err != nil {
+				return err
+			}
+		}
+
+		// Run the matrix.
+		runc := execCommand("runc", "run", "borg-container")
+		runc.Dir = tempDir
+		runc.Stdout = os.Stdout
+		runc.Stderr = os.Stderr
+		runc.Stdin = os.Stdin
+		return runc.Run()
+	},
+}
+
+func init() {
+	RootCmd.AddCommand(runCmd)
+}
diff --git a/cmd/run_test.go b/cmd/run_test.go
new file mode 100644
index 0000000..bec33fc
--- /dev/null
+++ b/cmd/run_test.go
@@ -0,0 +1,77 @@
+package cmd
+
+import (
+	"archive/tar"
+	"os"
+	"os/exec"
+	"path/filepath"
+	"testing"
+
+	"github.com/Snider/Borg/pkg/matrix"
+)
+
+func helperProcess(command string, args ...string) *exec.Cmd {
+	cs := []string{"-test.run=TestHelperProcess", "--", command}
+	cs = append(cs, args...)
+	cmd := exec.Command(os.Args[0], cs...)
+	cmd.Env = []string{"GO_WANT_HELPER_PROCESS=1"}
+	return cmd
+}
+
+func TestHelperProcess(t *testing.T) {
+	if os.Getenv("GO_WANT_HELPER_PROCESS") != "1" {
+		return
+	}
+	os.Exit(0)
+}
+
+func TestRunCmd_Good(t *testing.T) {
+	// Create a dummy matrix file.
+	tempDir := t.TempDir()
+	matrixPath := filepath.Join(tempDir, "test.matrix")
+	matrixFile, err := os.Create(matrixPath)
+	if err != nil {
+		t.Fatalf("failed to create dummy matrix file: %v", err)
+	}
+	defer matrixFile.Close()
+
+	tw := tar.NewWriter(matrixFile)
+	// Add a dummy config.json.
+	configContent := []byte(matrix.DefaultConfigJSON)
+	hdr := &tar.Header{
+		Name: "config.json",
+		Mode: 0600,
+		Size: int64(len(configContent)),
+	}
+	if err := tw.WriteHeader(hdr); err != nil {
+		t.Fatalf("failed to write tar header: %v", err)
+	}
+	if _, err := tw.Write(configContent); err != nil {
+		t.Fatalf("failed to write tar content: %v", err)
+	}
+
+	// Add the rootfs directory.
+	hdr = &tar.Header{
+		Name:     "rootfs/",
+		Mode:     0755,
+		Typeflag: tar.TypeDir,
+	}
+	if err := tw.WriteHeader(hdr); err != nil {
+		t.Fatalf("failed to write tar header: %v", err)
+	}
+
+	if err := tw.Close(); err != nil {
+		t.Fatalf("failed to close tar writer: %v", err)
+	}
+
+	// Mock the exec.Command function.
+	execCommand = helperProcess
+
+	// Run the run command.
+	rootCmd := NewRootCmd()
+	rootCmd.AddCommand(runCmd)
+	_, err = executeCommand(rootCmd, "run", matrixPath)
+	if err != nil {
+		t.Fatalf("run command failed: %v", err)
+	}
+}
diff --git a/pkg/matrix/config.go b/pkg/matrix/config.go
index 3ba19f3..80d9ab5 100644
--- a/pkg/matrix/config.go
+++ b/pkg/matrix/config.go
@@ -5,7 +5,7 @@ import (
 )
 
 // This is the default runc spec, generated by `runc spec`.
-const defaultConfigJSON = `{
+const DefaultConfigJSON = `{
 	"ociVersion": "1.2.1",
 	"process": {
 		"terminal": true,
@@ -79,7 +79,7 @@ const defaultConfigJSON = `{
 				"newinstance",
 				"ptmxmode=0666",
 				"mode=0620",
-				"gid":5
+				"gid=5"
 			]
 		},
 		{
@@ -182,7 +182,7 @@ const defaultConfigJSON = `{
 // defaultConfig returns the default runc spec.
 func defaultConfig() (map[string]interface{}, error) {
 	var spec map[string]interface{}
-	err := json.Unmarshal([]byte(defaultConfigJSON), &spec)
+	err := json.Unmarshal([]byte(DefaultConfigJSON), &spec)
 	if err != nil {
 		return nil, err
 	}
diff --git a/pkg/matrix/matrix.go b/pkg/matrix/matrix.go
index 3738577..ef15bec 100644
--- a/pkg/matrix/matrix.go
+++ b/pkg/matrix/matrix.go
@@ -63,6 +63,16 @@ func (m *TerminalIsolationMatrix) ToTar() ([]byte, error) {
 		return nil, err
 	}
 
+	// Add the rootfs directory.
+	hdr = &tar.Header{
+		Name:     "rootfs/",
+		Mode:     0755,
+		Typeflag: tar.TypeDir,
+	}
+	if err := tw.WriteHeader(hdr); err != nil {
+		return nil, err
+	}
+
 	// Add the rootfs files.
 	err := m.RootFS.Walk(".", func(path string, d fs.DirEntry, err error) error {
 		if err != nil {