diff --git a/AGENTS.md b/AGENTS.md
index 2623e9b..b8547af 100644
--- a/AGENTS.md
+++ b/AGENTS.md
@@ -57,6 +57,7 @@ This repository publishes the open-source server, console, integration catalog,
 - Preserve the minimum runtime versions declared by each package.
 - Keep private keys and API tokens out of process arguments and generated setup commands. Accept them through hidden terminal input or owner-only credential files.
 - Persist credential-bearing files through owner-only same-directory temporary files and atomic rename.
+- Resolve every agent runtime directory as one physical child of `~/.elydora`; reject separators, traversal segments, cross-platform reserved names, symbolic-link directories, and linked identity configs before writes or recursive removal. Validate stored directory identity before changing host CLI configuration, and require an explicit agent ID when discovery is ambiguous.
 
 ## Verification
 
diff --git a/sdks/node/README.md b/sdks/node/README.md
index b64f1b3..41b2584 100644
--- a/sdks/node/README.md
+++ b/sdks/node/README.md
@@ -51,7 +51,7 @@ npx elydora install \
   --kid agent-456-key-v1
 ```
 
-The CLI reads the private key and optional API token through hidden terminal prompts. For non-interactive installation, store each secret in an owner-only file and pass `--private_key_file <path>` and `--token_file <path>`. Secret values are rejected as command-line arguments because process listings and shell history can expose them.
+The CLI reads the private key and optional API token through hidden terminal prompts. For non-interactive installation, store each secret in an owner-only file and pass `--private_key_file <path>` and `--token_file <path>`. Secret values are rejected as command-line arguments because process listings and shell history can expose them. Agent IDs map to one physical directory directly under `~/.elydora`; portable filename rules and physical-directory checks apply before writes or recursive removal. Ambiguous uninstall discovery requires an explicit agent ID.
 
 Codex performs a one-time trust review for user hooks. Run `/hooks` in Codex after installation and trust the Elydora `PreToolUse` and `PostToolUse` definitions.
 
diff --git a/sdks/node/src/cli.ts b/sdks/node/src/cli.ts
index f1d48cf..a0633bf 100644
--- a/sdks/node/src/cli.ts
+++ b/sdks/node/src/cli.ts
@@ -4,7 +4,13 @@ import path from 'node:path';
 import os from 'node:os';
 import { resolveInstallSecrets } from './cli-secrets.js';
 import { derivePublicKey } from './crypto.js';
-import { ensurePrivateDirectory, writePrivateFile } from './secure-files.js';
+import {
+  ensurePrivateDirectory,
+  requirePhysicalDirectory,
+  requirePhysicalFile,
+  resolvePrivateChildDirectory,
+} from './runtime-paths.js';
+import { writePrivateFile } from './secure-files.js';
 import { SUPPORTED_AGENTS } from './plugins/registry.js';
 import type { AgentPlugin, InstallConfig } from './plugins/base.js';
 import { generateHookScript, generateGuardScript } from './plugins/hook-template.js';
@@ -53,6 +59,65 @@ function die(message: string): never {
   process.exit(1);
 }
 
+interface InstalledAgent {
+  agentId: string;
+  agentName: string;
+  configPath: string;
+}
+
+function isRecord(value: unknown): value is Record<string, unknown> {
+  return typeof value === 'object' && value !== null && !Array.isArray(value);
+}
+
+async function readInstalledAgent(agentId: string): Promise<InstalledAgent | undefined> {
+  const agentDirectory = resolvePrivateChildDirectory(ELYDORA_DIR, agentId);
+  if (!(await requirePhysicalDirectory(agentDirectory))) return undefined;
+
+  const configPath = path.join(agentDirectory, 'config.json');
+  if (!(await requirePhysicalFile(configPath))) return undefined;
+  let raw: string;
+  try {
+    raw = await fsp.readFile(configPath, 'utf-8');
+  } catch (error) {
+    throw new Error(`Could not read agent config: ${configPath}`, { cause: error });
+  }
+
+  let config: unknown;
+  try {
+    config = JSON.parse(raw);
+  } catch (error) {
+    throw new Error(`Could not parse agent config: ${configPath}`, { cause: error });
+  }
+  if (
+    !isRecord(config)
+    || typeof config.agent_id !== 'string'
+    || typeof config.agent_name !== 'string'
+  ) {
+    throw new Error(`Agent config has an invalid runtime identity: ${configPath}`);
+  }
+  if (config.agent_id !== agentId) {
+    throw new Error(`Agent config crosses its runtime directory: ${configPath}`);
+  }
+  resolvePrivateChildDirectory(ELYDORA_DIR, config.agent_id);
+  return { agentId, agentName: config.agent_name, configPath };
+}
+
+async function discoverInstalledAgents(): Promise<InstalledAgent[]> {
+  if (!(await requirePhysicalDirectory(ELYDORA_DIR))) return [];
+
+  const entries = await fsp.readdir(ELYDORA_DIR, { withFileTypes: true });
+  const installedAgents: InstalledAgent[] = [];
+  for (const entry of entries) {
+    if (entry.isSymbolicLink()) {
+      throw new Error(`Agent runtime path is not a physical directory: ${path.join(ELYDORA_DIR, entry.name)}`);
+    }
+    if (!entry.isDirectory()) continue;
+    const installedAgent = await readInstalledAgent(entry.name);
+    if (installedAgent) installedAgents.push(installedAgent);
+  }
+  return installedAgents;
+}
+
 function printUsage(): void {
   console.log(`Elydora CLI — Tamper-evident audit for AI coding agents
 
@@ -102,6 +167,7 @@ async function cmdInstall(args: string[]): Promise<void> {
 
   const agentId = values.agent_id;
   if (!agentId) die('--agent_id is required');
+  const agentDir = resolvePrivateChildDirectory(ELYDORA_DIR, agentId);
 
   const kid = values.kid;
   if (!kid) die('--kid is required');
@@ -123,7 +189,6 @@ async function cmdInstall(args: string[]): Promise<void> {
   console.log(`Verifying private key... Public key: ${publicKey.slice(0, 12)}...`);
 
   // Create ~/.elydora/{agentId}/ directory
-  const agentDir = path.join(ELYDORA_DIR, agentId);
   await ensurePrivateDirectory(ELYDORA_DIR);
   await ensurePrivateDirectory(agentDir);
 
@@ -194,31 +259,36 @@ async function cmdUninstall(args: string[]): Promise<void> {
   }
 
   let agentId = values.agent_id;
+  let agentDir: string;
+  let agentDirectoryExists: boolean;
 
   // If --agent_id not provided, scan ~/.elydora/*/config.json for matching agent_name
-  if (!agentId) {
-    try {
-      const entries = await fsp.readdir(ELYDORA_DIR, { withFileTypes: true });
-      for (const entry of entries) {
-        if (!entry.isDirectory()) continue;
-        const cfgPath = path.join(ELYDORA_DIR, entry.name, 'config.json');
-        try {
-          const raw = await fsp.readFile(cfgPath, 'utf-8');
-          const cfg = JSON.parse(raw);
-          if (cfg.agent_name === agentName) {
-            agentId = entry.name;
-            break;
-          }
-        } catch {
-          // Skip unreadable configs
-        }
+  if (agentId) {
+    agentDir = resolvePrivateChildDirectory(ELYDORA_DIR, agentId);
+    const runtimeRootExists = await requirePhysicalDirectory(ELYDORA_DIR);
+    agentDirectoryExists = runtimeRootExists
+      ? await requirePhysicalDirectory(agentDir)
+      : false;
+    if (agentDirectoryExists) {
+      const installedAgent = await readInstalledAgent(agentId);
+      if (installedAgent && installedAgent.agentName !== agentName) {
+        throw new Error(
+          `Agent runtime ${agentId} belongs to ${installedAgent.agentName}, not ${agentName}`,
+        );
       }
-    } catch {
-      // ELYDORA_DIR may not exist
     }
-    if (!agentId) {
+  } else {
+    const matches = (await discoverInstalledAgents())
+      .filter((installedAgent) => installedAgent.agentName === agentName);
+    if (matches.length === 0) {
       die(`No installed agent found for "${agentName}". Use --agent_id to specify explicitly.`);
     }
+    if (matches.length > 1) {
+      die(`Multiple installed agents found for "${agentName}". Use --agent_id to specify explicitly.`);
+    }
+    agentId = matches[0].agentId;
+    agentDir = resolvePrivateChildDirectory(ELYDORA_DIR, agentId);
+    agentDirectoryExists = true;
   }
 
   const plugin = PLUGINS.get(agentName)!;
@@ -228,11 +298,8 @@ async function cmdUninstall(args: string[]): Promise<void> {
   await plugin.uninstall(agentId);
 
   // Remove entire agent directory
-  const agentDir = path.join(ELYDORA_DIR, agentId);
-  try {
-    await fsp.rm(agentDir, { recursive: true, force: true });
-  } catch {
-    // Already removed
+  if (agentDirectoryExists) {
+    await fsp.rm(agentDir, { recursive: true });
   }
 
   console.log(`Elydora audit hook uninstalled for ${registryEntry.name}.`);
@@ -244,25 +311,7 @@ async function cmdStatus(): Promise<void> {
   let anyInstalled = false;
 
   // Scan ~/.elydora/*/config.json to discover installed agents
-  const installedAgents: Array<{ agentId: string; agentName: string; configPath: string }> = [];
-  try {
-    const entries = await fsp.readdir(ELYDORA_DIR, { withFileTypes: true });
-    for (const entry of entries) {
-      if (!entry.isDirectory()) continue;
-      const cfgPath = path.join(ELYDORA_DIR, entry.name, 'config.json');
-      try {
-        const raw = await fsp.readFile(cfgPath, 'utf-8');
-        const cfg = JSON.parse(raw);
-        if (cfg.agent_name && cfg.agent_id) {
-          installedAgents.push({ agentId: entry.name, agentName: cfg.agent_name, configPath: cfgPath });
-        }
-      } catch {
-        // Skip unreadable configs
-      }
-    }
-  } catch {
-    // ELYDORA_DIR may not exist
-  }
+  const installedAgents = await discoverInstalledAgents();
 
   for (const [name, plugin] of PLUGINS) {
     const st = await plugin.status();
diff --git a/sdks/node/src/runtime-paths.ts b/sdks/node/src/runtime-paths.ts
new file mode 100644
index 0000000..279cada
--- /dev/null
+++ b/sdks/node/src/runtime-paths.ts
@@ -0,0 +1,77 @@
+import fsp from 'node:fs/promises';
+import path from 'node:path';
+
+export function isMissingPath(error: unknown): boolean {
+  return error instanceof Error && 'code' in error && error.code === 'ENOENT';
+}
+
+export async function ensurePrivateDirectory(directory: string): Promise<void> {
+  await fsp.mkdir(directory, { recursive: true, mode: 0o700 });
+  const metadata = await fsp.lstat(directory);
+  if (!metadata.isDirectory() || metadata.isSymbolicLink()) {
+    throw new Error(`Private directory path is not a physical directory: ${directory}`);
+  }
+  if (process.platform !== 'win32') {
+    await fsp.chmod(directory, 0o700);
+  }
+}
+
+export async function requirePhysicalDirectory(directory: string): Promise<boolean> {
+  let metadata;
+  try {
+    metadata = await fsp.lstat(directory);
+  } catch (error) {
+    if (isMissingPath(error)) return false;
+    throw new Error(`Could not inspect agent runtime directory: ${directory}`, { cause: error });
+  }
+  if (!metadata.isDirectory() || metadata.isSymbolicLink()) {
+    throw new Error(`Agent runtime path is not a physical directory: ${directory}`);
+  }
+  return true;
+}
+
+export async function requirePhysicalFile(filePath: string): Promise<boolean> {
+  let metadata;
+  try {
+    metadata = await fsp.lstat(filePath);
+  } catch (error) {
+    if (isMissingPath(error)) return false;
+    throw new Error(`Could not inspect agent runtime file: ${filePath}`, { cause: error });
+  }
+  if (!metadata.isFile() || metadata.isSymbolicLink()) {
+    throw new Error(`Agent runtime config is not a physical file: ${filePath}`);
+  }
+  return true;
+}
+
+export function resolvePrivateChildDirectory(root: string, childName: string): string {
+  const isWindowsDeviceName = /^(?:con|prn|aux|nul|com[1-9¹²³]|lpt[1-9¹²³])(?:\.|$)/i.test(childName);
+  if (
+    childName.length === 0
+    || /[<>:"|?*\u0000-\u001f]/.test(childName)
+    || childName.includes('/')
+    || childName.includes('\\')
+    || childName === '.'
+    || childName === '..'
+    || childName.startsWith(' ')
+    || childName.endsWith('.')
+    || childName.endsWith(' ')
+    || isWindowsDeviceName
+  ) {
+    throw new Error(`Invalid agent ID for local storage: ${JSON.stringify(childName)}`);
+  }
+
+  const resolvedRoot = path.resolve(root);
+  const candidate = path.resolve(resolvedRoot, childName);
+  const relative = path.relative(resolvedRoot, candidate);
+  if (
+    relative.length === 0
+    || path.isAbsolute(relative)
+    || relative === '..'
+    || relative.startsWith(`..${path.sep}`)
+    || relative.includes(path.sep)
+  ) {
+    throw new Error(`Agent ID escapes the local storage directory: ${JSON.stringify(childName)}`);
+  }
+  return candidate;
+}
diff --git a/sdks/node/src/secure-files.ts b/sdks/node/src/secure-files.ts
index 9dc19c6..3662ceb 100644
--- a/sdks/node/src/secure-files.ts
+++ b/sdks/node/src/secure-files.ts
@@ -1,17 +1,7 @@
 import crypto from 'node:crypto';
 import fsp from 'node:fs/promises';
 import path from 'node:path';
-
-function isMissingFile(error: unknown): boolean {
-  return error instanceof Error && 'code' in error && error.code === 'ENOENT';
-}
-
-export async function ensurePrivateDirectory(directory: string): Promise<void> {
-  await fsp.mkdir(directory, { recursive: true, mode: 0o700 });
-  if (process.platform !== 'win32') {
-    await fsp.chmod(directory, 0o700);
-  }
-}
+import { ensurePrivateDirectory, isMissingPath } from './runtime-paths.js';
 
 export async function writePrivateFile(filePath: string, contents: string): Promise<void> {
   const directory = path.dirname(filePath);
@@ -41,7 +31,7 @@ export async function writePrivateFile(filePath: string, contents: string): Prom
       try {
         await fsp.unlink(temporaryPath);
       } catch (error) {
-        if (!isMissingFile(error)) throw error;
+        if (!isMissingPath(error)) throw error;
       }
     }
   }
diff --git a/sdks/node/test/cli-security.test.mjs b/sdks/node/test/cli-security.test.mjs
index 897672e..fdb7e81 100644
--- a/sdks/node/test/cli-security.test.mjs
+++ b/sdks/node/test/cli-security.test.mjs
@@ -1,11 +1,12 @@
 import assert from 'node:assert/strict';
-import { chmod, mkdtemp, readFile, rm, stat, writeFile } from 'node:fs/promises';
+import { chmod, mkdir, mkdtemp, readFile, rm, stat, symlink, writeFile } from 'node:fs/promises';
 import os from 'node:os';
 import path from 'node:path';
 import { spawn } from 'node:child_process';
 import test from 'node:test';
 
 import { resolveInstallSecrets } from '../dist/cli-secrets.js';
+import { requirePhysicalDirectory } from '../dist/runtime-paths.js';
 
 const PRIVATE_KEY = Buffer.alloc(32, 7).toString('base64url');
 const API_TOKEN = 'ely_test_token';
@@ -102,6 +103,151 @@ test('CLI rejects legacy secret arguments before writing files', async () => {
   }
 });
 
+test('CLI rejects agent IDs that escape the credential directory', async () => {
+  const invalidAgentIds = [
+    '../escape',
+    '..\\escape',
+    'C:escape',
+    'agent.',
+    'agent ',
+    ' agent',
+    'CON',
+    'COM¹.log',
+    '.',
+    '..',
+  ];
+  for (const agentId of invalidAgentIds) {
+    const homeDir = await mkdtemp(path.join(os.tmpdir(), 'elydora-node-cli-'));
+    try {
+      const result = await runCli([
+        'install',
+        '--agent', 'opencode',
+        '--org_id', 'org-1',
+        '--agent_id', agentId,
+        '--kid', 'key-1',
+      ], homeDir);
+
+      assert.equal(result.code, 1);
+      assert.match(result.stderr, /(Invalid agent ID for local storage|Agent ID escapes)/);
+      await assert.rejects(stat(path.join(homeDir, '.elydora')), { code: 'ENOENT' });
+    } finally {
+      await rm(homeDir, { recursive: true, force: true });
+    }
+  }
+});
+
+test('uninstall validates the stored runtime identity before plugin changes', async () => {
+  const homeDir = await mkdtemp(path.join(os.tmpdir(), 'elydora-node-cli-'));
+  const runtimeDir = path.join(homeDir, '.elydora', 'stored-directory');
+  try {
+    await mkdir(runtimeDir, { recursive: true });
+    await writeFile(
+      path.join(runtimeDir, 'config.json'),
+      JSON.stringify({ agent_name: 'opencode', agent_id: 'different-agent' }),
+      'utf-8',
+    );
+    const result = await runCli(['uninstall', '--agent', 'opencode'], homeDir);
+
+    assert.equal(result.code, 1);
+    assert.match(result.stderr, /crosses its runtime directory/);
+    assert.equal((await stat(runtimeDir)).isDirectory(), true);
+  } finally {
+    await rm(homeDir, { recursive: true, force: true });
+  }
+});
+
+test('uninstall requires an explicit ID for ambiguous agent runtimes', async () => {
+  const homeDir = await mkdtemp(path.join(os.tmpdir(), 'elydora-node-cli-'));
+  try {
+    for (const agentId of ['agent-1', 'agent-2']) {
+      const runtimeDir = path.join(homeDir, '.elydora', agentId);
+      await mkdir(runtimeDir, { recursive: true });
+      await writeFile(
+        path.join(runtimeDir, 'config.json'),
+        JSON.stringify({ agent_name: 'opencode', agent_id: agentId }),
+        'utf-8',
+      );
+    }
+    const result = await runCli(['uninstall', '--agent', 'opencode'], homeDir);
+
+    assert.equal(result.code, 1);
+    assert.match(result.stderr, /Multiple installed agents/);
+    assert.equal((await stat(path.join(homeDir, '.elydora', 'agent-1'))).isDirectory(), true);
+    assert.equal((await stat(path.join(homeDir, '.elydora', 'agent-2'))).isDirectory(), true);
+  } finally {
+    await rm(homeDir, { recursive: true, force: true });
+  }
+});
+
+test('runtime directory checks reject symbolic-link children', async (t) => {
+  const homeDir = await mkdtemp(path.join(os.tmpdir(), 'elydora-node-cli-'));
+  const targetDir = await mkdtemp(path.join(os.tmpdir(), 'elydora-node-target-'));
+  const runtimeRoot = path.join(homeDir, '.elydora');
+  const linkPath = path.join(runtimeRoot, 'agent-1');
+  try {
+    await mkdir(runtimeRoot, { recursive: true });
+    try {
+      await symlink(targetDir, linkPath, 'dir');
+    } catch (error) {
+      t.skip(`Directory symbolic links are unavailable: ${error.message}`);
+      return;
+    }
+
+    await assert.rejects(
+      requirePhysicalDirectory(linkPath),
+      /not a physical directory/,
+    );
+  } finally {
+    await rm(homeDir, { recursive: true, force: true });
+    await rm(targetDir, { recursive: true, force: true });
+  }
+});
+
+test('status surfaces malformed runtime config', async () => {
+  const homeDir = await mkdtemp(path.join(os.tmpdir(), 'elydora-node-cli-'));
+  const runtimeDir = path.join(homeDir, '.elydora', 'agent-1');
+  try {
+    await mkdir(runtimeDir, { recursive: true });
+    await writeFile(path.join(runtimeDir, 'config.json'), '{invalid-json', 'utf-8');
+
+    const result = await runCli(['status'], homeDir);
+
+    assert.equal(result.code, 1);
+    assert.match(result.stderr, /Could not parse agent config/);
+  } finally {
+    await rm(homeDir, { recursive: true, force: true });
+  }
+});
+
+test('status rejects symbolic-link runtime configs', async (t) => {
+  const homeDir = await mkdtemp(path.join(os.tmpdir(), 'elydora-node-cli-'));
+  const targetDir = await mkdtemp(path.join(os.tmpdir(), 'elydora-node-target-'));
+  const runtimeDir = path.join(homeDir, '.elydora', 'agent-1');
+  const targetConfig = path.join(targetDir, 'config.json');
+  try {
+    await mkdir(runtimeDir, { recursive: true });
+    await writeFile(
+      targetConfig,
+      JSON.stringify({ agent_name: 'opencode', agent_id: 'agent-1' }),
+      'utf-8',
+    );
+    try {
+      await symlink(targetConfig, path.join(runtimeDir, 'config.json'), 'file');
+    } catch (error) {
+      t.skip(`File symbolic links are unavailable: ${error.message}`);
+      return;
+    }
+
+    const result = await runCli(['status'], homeDir);
+
+    assert.equal(result.code, 1);
+    assert.match(result.stderr, /runtime config is not a physical file/);
+  } finally {
+    await rm(homeDir, { recursive: true, force: true });
+    await rm(targetDir, { recursive: true, force: true });
+  }
+});
+
 test('CLI installs from owner-only files and protects persisted credentials', async () => {
   const homeDir = await mkdtemp(path.join(os.tmpdir(), 'elydora-node-cli-'));
   const privateKeyFile = path.join(homeDir, 'private-key');