Add security allowlist for command execution and update copilot instructions

- Add security.ts with allowlist configuration for shell commands
- Update command-executor.ts to enforce security policy (exit code 126 for blocked commands)
- Update copilot instructions to clarify builtin tools vs shell commands
- Document that builtin tools (deleteFile, createFile, etc.) bypass security filtering
- Only executeCommand (shell commands) requires security.json allowlist entries

apps/cli/src/application/config/security.ts

@@ -0,0 +1,90 @@
+import path from "path";
+import fs from "fs";
+import { WorkDir } from "./config.js";
+
+export const SECURITY_CONFIG_PATH = path.join(WorkDir, "config", "security.json");
+
+const DEFAULT_ALLOW_LIST = ["ls", "pwd", "cat", "echo", "whoami"];
+
+let cachedAllowList: string[] | null = null;
+let cachedMtimeMs: number | null = null;
+
+function ensureSecurityConfig() {
+    if (!fs.existsSync(SECURITY_CONFIG_PATH)) {
+        fs.writeFileSync(
+            SECURITY_CONFIG_PATH,
+            JSON.stringify(DEFAULT_ALLOW_LIST, null, 2) + "\n",
+            "utf8",
+        );
+    }
+}
+
+function normalizeList(commands: unknown[]): string[] {
+    const seen = new Set<string>();
+    for (const entry of commands) {
+        if (typeof entry !== "string") continue;
+        const normalized = entry.trim().toLowerCase();
+        if (!normalized) continue;
+        seen.add(normalized);
+    }
+
+    return Array.from(seen);
+}
+
+function parseSecurityPayload(payload: unknown): string[] {
+    if (Array.isArray(payload)) {
+        return normalizeList(payload);
+    }
+
+    if (payload && typeof payload === "object") {
+        const maybeObject = payload as Record<string, unknown>;
+        if (Array.isArray(maybeObject.allowedCommands)) {
+            return normalizeList(maybeObject.allowedCommands);
+        }
+
+        const dynamicList = Object.entries(maybeObject)
+            .filter(([, value]) => Boolean(value))
+            .map(([key]) => key);
+
+        return normalizeList(dynamicList);
+    }
+
+    return [];
+}
+
+function readAllowList(): string[] {
+    ensureSecurityConfig();
+
+    try {
+        const configContent = fs.readFileSync(SECURITY_CONFIG_PATH, "utf8");
+        const parsed = JSON.parse(configContent);
+        return parseSecurityPayload(parsed);
+    } catch (error) {
+        console.warn(`Failed to read security config at ${SECURITY_CONFIG_PATH}: ${error instanceof Error ? error.message : error}`);
+        return DEFAULT_ALLOW_LIST;
+    }
+}
+
+export function getSecurityAllowList(): string[] {
+    ensureSecurityConfig();
+    try {
+        const stats = fs.statSync(SECURITY_CONFIG_PATH);
+        if (cachedAllowList && cachedMtimeMs === stats.mtimeMs) {
+            return cachedAllowList;
+        }
+
+        const allowList = readAllowList();
+        cachedAllowList = allowList;
+        cachedMtimeMs = stats.mtimeMs;
+        return allowList;
+    } catch {
+        cachedAllowList = null;
+        cachedMtimeMs = null;
+        return readAllowList();
+    }
+}
+
+export function resetSecurityAllowListCache() {
+    cachedAllowList = null;
+    cachedMtimeMs = null;
+}