diff --git a/.codex-plugin/README.md b/.codex-plugin/README.md
index ed4ece00e..64ade090e 100644
--- a/.codex-plugin/README.md
+++ b/.codex-plugin/README.md
@@ -77,6 +77,67 @@ Once the cached skills are available, invoke `$configure-ecc` inside Codex for
 ECC's guided configuration. Installing the plugin again is idempotent and does
 not create a second scope or duplicate hook registration.
 
+## Runtime dependencies and Codex 0.164.0 cache checks
+
+Native marketplace installation copies ECC's source; it does not run `npm ci`
+for its hook dependencies. If a hook reports a missing runtime package, first
+run `codex plugin list --json` with the same `CODEX_HOME` as the affected
+session. Find the installed, enabled `ecc@ecc` entry and its version; do not
+select a version merely because its directory exists. From an ECC checkout,
+check that version explicitly:
+
+```bash
+# Replace <installed-version> with the version from Codex's installed entry.
+node scripts/codex/check-plugin-cache.js --version '<installed-version>'
+```
+
+If the affected session's hook warning identifies the exact ECC plugin root,
+prefer `node scripts/codex/check-plugin-cache.js --plugin-dir "/absolute/path/to/active/ecc/cache"`.
+Use the same `CODEX_HOME` for the version check (or pass `--codex-home`). The
+checker's default comes from the checkout's `package.json`; it does not discover
+the active version, and a passing check against an older cache is insufficient.
+Confirm the selected root matches the affected session before installing. Do
+not use the deprecated sync script to repair the native plugin.
+
+Codex 0.164.0 can reject a plugin after a normal dependency install with
+`unsupported plugin entry type ... node_modules/.bin/js-yaml`. npm normally
+creates executable symlinks in `.bin`; that Codex version's hook fingerprint
+walker accepts only directories and regular files. See
+[ECC #3742](https://github.com/affaan-m/ECC/issues/3742) and the
+[Codex fingerprint implementation](https://github.com/openai/codex/blob/rust-v0.164.0/codex-rs/hooks/src/engine/plugin_fingerprint.rs).
+
+For an explicitly chosen cache-local dependency install, use npm's
+[`--no-bin-links`](https://docs.npmjs.com/cli/v11/commands/npm-ci#bin-links)
+option to install the runtime packages without creating executable links:
+
+```bash
+# Set this to the active ECC plugin root confirmed above.
+ECC_PLUGIN_CACHE="/absolute/path/to/active/ecc/cache"
+(
+  set -eu
+  cd -- "$ECC_PLUGIN_CACHE"
+  test -f package.json
+  test -f package-lock.json
+  npm ci --omit=dev --ignore-scripts --no-audit --no-fund --no-bin-links
+  node -e "require('js-yaml'); require('@iarna/toml'); require('ajv'); require('sql.js'); require('zod')"
+)
+```
+
+The cache root must contain ECC's `package.json` and `package-lock.json`. The
+subshell stops on a failed directory change, missing manifest, or failed install
+before running any later command, and leaves the caller's directory unchanged.
+`npm ci` replaces its dependency tree; this opt-in command is not part of the
+default Codex installer. The final command checks Node package resolution, not
+Codex hook execution. Executable shortcuts in `node_modules/.bin` are
+intentionally unavailable; ECC hooks load these packages through Node.
+
+Restart Codex, review the updated hook definitions in `/hooks`, and verify a
+new session's actual hook result. Do not disable fingerprint or trust checks.
+This addresses npm-generated executable links, not every possible unsupported
+cache entry or the upstream Codex defect. A marketplace refresh can replace
+cache-local changes; recheck the active version before applying the command
+again.
+
 ## Native plugin versus legacy managed sync
 
 The commands above are the native Codex plugin path. The deprecated legacy managed sync
@@ -93,11 +154,12 @@ history or native plugin caches. Older pre-manifest installs are cleaned
 conservatively and unverifiable files are retained with warnings.
 
 After install, `codex plugin list` is only a registration check. From an ECC
-checkout, run the cache check to verify that the installed manifest can resolve
-its referenced skills, MCP config, and assets:
+checkout, set `ECC_PLUGIN_CACHE` to the active root identified above, then run
+the cache check to verify that the installed manifest can resolve its referenced
+skills, MCP config, and assets:
 
 ```bash
-node scripts/codex/check-plugin-cache.js
+node scripts/codex/check-plugin-cache.js --plugin-dir "$ECC_PLUGIN_CACHE"
 ```
 
 The installed plugin registers under the short slug `ecc` so tool and command names
diff --git a/.codex/AGENTS.md b/.codex/AGENTS.md
index 9f6c5d28a..7ceffb283 100644
--- a/.codex/AGENTS.md
+++ b/.codex/AGENTS.md
@@ -5,6 +5,9 @@ This supplements the root `AGENTS.md` with Codex-specific guidance.
 For repo navigation, surface ownership, and PR diff packet guidance, read
 `docs/CODEX-NAVIGATION-GUIDE.md` after this supplement.
 
+For native cache dependency installation and Codex 0.164.0 executable-link
+rejections, use the [runtime dependency procedure](../.codex-plugin/README.md#runtime-dependencies-and-codex-01640-cache-checks).
+
 ## Model Recommendations
 
 | Task Type | Recommended Model |
diff --git a/README.md b/README.md
index 7e34937a9..80966f5b0 100644
--- a/README.md
+++ b/README.md
@@ -2114,6 +2114,10 @@ node scripts/codex/check-plugin-cache.js
 ```
 
 If it reports unresolved parent references, refresh the native cache with `codex plugin marketplace upgrade ecc`, run `codex plugin add ecc@ecc` again, and restart Codex. Registration in `codex plugin list` confirms the marketplace entry, while the cache check verifies that the installed manifest can resolve its skills, MCP configuration, and assets. Use `bash scripts/sync-ecc-to-codex.sh` only when you intentionally need the legacy copied-configuration compatibility path.
+
+If Codex 0.164.0 reports `unsupported plugin entry type` after you install hook
+dependencies into the cache, see the [cache-local runtime dependency procedure](.codex-plugin/README.md#runtime-dependencies-and-codex-01640-cache-checks).
+It avoids npm executable symlinks without disabling Codex's hook trust checks.
 </details>
 
 More answers: [TROUBLESHOOTING.md](TROUBLESHOOTING.md) covers memory, hooks, installation, performance, and common error messages. [docs/TROUBLESHOOTING.md](docs/TROUBLESHOOTING.md) tracks workarounds for open Claude Code bugs.
diff --git a/scripts/codex/check-plugin-cache.js b/scripts/codex/check-plugin-cache.js
index 0a21cc48f..e293ae5b3 100644
--- a/scripts/codex/check-plugin-cache.js
+++ b/scripts/codex/check-plugin-cache.js
@@ -227,13 +227,15 @@ function checkCache(options) {
   if (failures > 0) {
     log(`${failures} cached manifest reference(s) do not resolve.`);
     log('codex plugin list only confirms marketplace registration; it is not proof of runtime skill loading.');
-    const syncScript = path.join(REPO_ROOT, 'scripts', 'sync-ecc-to-codex.sh');
-    if (fs.existsSync(syncScript)) {
-      log('Use the supported sync path until the cache contains the referenced files:');
-      log('npm install && bash scripts/sync-ecc-to-codex.sh');
+    log('Refresh the native marketplace and re-add the plugin using the same CODEX_HOME as the affected session:');
+    if (options.marketplace === 'ecc' && options.plugin === 'ecc') {
+      log('codex plugin marketplace upgrade ecc');
+      log('codex plugin add ecc@ecc');
     } else {
-      log('Use the supported manual sync workflow from your ECC installation.');
+      log('Follow the requested plugin marketplace instructions to refresh and re-add that native plugin.');
     }
+    log('Restart Codex, confirm the active plugin root with codex plugin list --json, and re-run this checker with --plugin-dir ACTIVE_ROOT (or --version ACTIVE_VERSION).');
+    log('See .codex-plugin/README.md for native cache recovery and runtime dependency instructions.');
     return 1;
   }
 
diff --git a/tests/scripts/codex-hooks.test.js b/tests/scripts/codex-hooks.test.js
index 007b98cfa..43830f6ff 100644
--- a/tests/scripts/codex-hooks.test.js
+++ b/tests/scripts/codex-hooks.test.js
@@ -660,7 +660,13 @@ if (
       assert.match(result.stdout, /\[FAIL\] skills missing/);
       assert.match(result.stdout, /\[FAIL\] mcpServers missing/);
       assert.match(result.stdout, /codex plugin list only confirms marketplace registration/);
-      assert.match(result.stdout, /sync-ecc-to-codex\.sh/);
+      assert.match(result.stdout, /codex plugin marketplace upgrade ecc/);
+      assert.match(result.stdout, /codex plugin add ecc@ecc/);
+      assert.match(result.stdout, /same CODEX_HOME/);
+      assert.match(result.stdout, /active plugin root/);
+      assert.match(result.stdout, /--plugin-dir ACTIVE_ROOT/);
+      assert.match(result.stdout, /--version ACTIVE_VERSION/);
+      assert.doesNotMatch(result.stdout, /npm install|sync-ecc-to-codex\.sh/);
     } finally {
       cleanup(homeDir);
     }