[BUG] Enterprise-managed marketplaces in project enabledPlugins are orphaned on first run; only install after a restart

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

On a fresh Claude Code install, plugins listed in a project's .claude/settings.json enabledPlugins that come from marketplaces delivered via remote managed settings (enterprise "allowed marketplace list") do not install on first launch. They only appear after one or more restarts. Root cause appears to be an ordering/race: the authorizing policy is fetched after authentication, and the in-process plugin reconcile runs before that policy + marketplace registration exist, then never completes in-process.

Environment

• Version: 2.1.158 at launch, auto-updated to 2.1.159 mid-session
• Platform: Linux (amzn2023)
• Auth: Anthropic OAuth, enterprise remote managed settings in use
• Project .claude/settings.json referenced plugins from xxxx-dev / xxxx2-product marketplaces (both delivered via the org's allowed-marketplace policy)

Observed sequence (from ~/.claude/debug/<session>.txt)

1. First launch (PID A, v2.1.158): installed_plugins.json absent; no company marketplaces registered yet. enabledPlugins entries skipped:

• Skipping orphaned enabledPlugins entry infra-provisioning@xxxx-dev: marketplace not registered
• Found 0 plugins (0 enabled, 0 disabled)

1. After auth, the policy arrives — but the first background install pass already ran:

• Remote settings: Refreshed after auth change / Programmatic settings change notification for policySettings
• First performBackgroundPluginInstallations → not found in any marketplace, skipping → Saved 0 installed plugins

1. Concurrent auto-update to 2.1.159 + relaunch (PID B). Plugin load races the allowlist:

• Plugin not available for MCP: …@xxxx-dev - error type: marketplace-blocked-by-policy
• Plugin loading errors: Marketplace 'xxxx-dev' is not in the allowed marketplace list
• …then git clone … succeeded → Added marketplace source: xxxx-dev (registered, but still Loaded 0 installed plugins this process)

1. Next relaunch (PID C): now policy cached + marketplaces registered → Saved 3 installed plugins / Sync completed: 3 added. Plugins finally work.

Expected

After the post-auth remote-settings refresh adds newly-allowed marketplaces, the plugin reconcile should complete in-process and install the enabledPlugins, without requiring a restart.

Actual

enabledPlugins referencing policy-gated marketplaces are orphaned on first run and only resolve after restart(s), because (a) the allowed-marketplace policy is fetched only post-auth and (b) the install pass that runs before/around that doesn't re-reconcile to completion (visible "blocked-by-policy" race even in the post-update process).

Impact

Confusing first-run onboarding for enterprise users with managed marketplaces — plugins/skills silently absent until an unprompted restart.

What Should Happen?

The marketplaces and the plugins are installed without a CC restart.

Error Messages/Logs

Steps to Reproduce

1. Start from a clean Claude Code install (no ~/.claude/plugins/installed_plugins.json, no private marketplaces in known_marketplaces.json).
2. Open a project whose .claude/settings.json lists enabledPlugins from a marketplace that is delivered/authorized via enterprise remote managed settings (not yet registered locally), e.g.:

"enabledPlugins": {
"plugin-a@org-dev": true,
"plugin-b@org-product": true
}

1. Launch Claude Code and complete first-run onboarding + authentication.
2. After login, open /plugin (or check installed_plugins.json).

• Result: No plugins installed. Debug log shows Skipping orphaned enabledPlugins entry … : marketplace not registered and Found 0 plugins, even though the post-auth Remote settings: Refreshed after auth

change has fired and authorized those marketplaces.

1. Restart Claude Code (once or twice).

• Result: Marketplaces register and plugins install (Saved N installed plugins).

Claude Model

None

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.1.159 (Claude Code)

Platform

Anthropic API

Operating System

Ubuntu/Debian Linux

Terminal/Shell

Other

Additional Information

uname -a
Linux ip-10-40-243-81.eu-west-1.compute.internal 6.12.88-119.157.amzn2023.x86_64 #1 SMP PREEMPT_DYNAMIC Wed May 20 06:36:23 UTC 2026 x86_64 x86_64 x86_64 GNU/Linux