diff --git a/cmd/nerd/cmd_advanced.go b/cmd/nerd/cmd_advanced.go
index 4c0251bb..95454cb4 100644
--- a/cmd/nerd/cmd_advanced.go
+++ b/cmd/nerd/cmd_advanced.go
@@ -7,6 +7,7 @@ import (
 	"fmt"
 	"os"
 	"os/exec"
+	"path/filepath"
 	"strings"
 	"time"
 
@@ -454,8 +455,35 @@ func runToolCommand(cmd *cobra.Command, args []string) error {
 			return fmt.Errorf("tool '%s' not found. Run 'nerd tool list' to see available tools", toolName)
 		}
 
+		// SECURITY FIX: Prevent command injection and path traversal
+		// Ensure the binary is executed from the .nerd/tools/.compiled directory
+		ws := workspace
+		if ws == "" {
+			ws, _ = os.Getwd()
+		}
+		expectedDir := filepath.Join(ws, ".nerd", "tools", ".compiled")
+
+		absExpectedDir, err := filepath.Abs(expectedDir)
+		if err != nil {
+			return fmt.Errorf("failed to resolve expected tools directory: %w", err)
+		}
+
+		absBinaryPath, err := filepath.Abs(binaryPath)
+		if err != nil {
+			return fmt.Errorf("failed to resolve binary path: %w", err)
+		}
+
+		relPath, err := filepath.Rel(absExpectedDir, absBinaryPath)
+		if err != nil || strings.HasPrefix(relPath, "..") || relPath == ".." || filepath.IsAbs(relPath) {
+			return fmt.Errorf("security error: binary path '%s' is outside expected directory '%s'", binaryPath, expectedDir)
+		}
+
+		if _, err := os.Stat(absBinaryPath); os.IsNotExist(err) {
+			return fmt.Errorf("tool binary not found at '%s'", absBinaryPath)
+		}
+
 		// Execute tool binary directly
-		toolCmd := exec.CommandContext(ctx, binaryPath)
+		toolCmd := exec.CommandContext(ctx, absBinaryPath)
 		if toolInput != "" {
 			toolCmd.Stdin = strings.NewReader(toolInput)
 		}
diff --git a/pr_description.txt b/pr_description.txt
index b4306963..a9d9df18 100644
--- a/pr_description.txt
+++ b/pr_description.txt
@@ -1,11 +1,6 @@
-**Title**: ⚡ Optimize AtomLoader.ReplaceAtoms with batch inserts to fix N+1 issue
+**Title**: 🔒 Fix potential command injection/path traversal in nerd tool run
 
 **Description**:
-💡 **What:** Refactored `AtomLoader.ReplaceAtoms` to use a true chunked batch insert approach (using `INSERT INTO ... VALUES (...), (...), ...`) and moved embedding generation out of the database transaction.
-
-🎯 **Why:** The previous implementation called `storeAtomTx` within a loop over atoms inside a database transaction. This resulted in an N+1 query problem, parsing and executing `INSERT` and redundant `DELETE` statements on a per-atom basis. Also, holding an open transaction while waiting on external network calls for embeddings generation is a significant anti-pattern that can lead to exhausted database connections and locks.
-
-📊 **Measured Improvement:**
-Before optimization, replacing 10,000 atoms took about 700ms, and 1,000 took about 84ms.
-After optimization using bulk chunk inserts, 1,000 atoms took about 23ms and 10,000 atoms took roughly 199ms.
-This represents a solid 3.5x to 3.6x measured performance improvement, alongside drastically improving the transaction health by removing network dependencies inside locks.
+🎯 **What**: Prevented unauthorized execution by validating the tool binary path before running it in `cmd/nerd/cmd_advanced.go`.
+⚠️ **Risk**: The previous code pulled `binaryPath` from a Mangle kernel fact `tool_binary_path` without checking if the binary actually belonged to the internal compiled tools directory. If an attacker managed to assert a malicious `tool_binary_path` (e.g. `../../../../bin/bash`), they could execute arbitrary binaries with the same privileges as the agent.
+🛡️ **Solution**: Ensure absolute path resolution for both the target binary and the expected directory (`.nerd/tools/.compiled`). Use `filepath.Rel` to explicitly verify that the binary resides strictly within the compiled directory, effectively preventing path traversal escapes and executing untrusted/unexpected binaries on the host system.