[BUG] `claude plugin install --scope project` overwrites `installed_plugins.json` instead of merging

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?

Each call to claude plugin install <plugin> --scope project overwrites ~/.claude/plugins/installed_plugins.json with a fresh single-entry file, erasing all previously registered plugins. After installing N plugins sequentially, only the last one survives in the registry.

The Plugins UI Errors tab then reports every project-scoped plugin as _"enabled in project settings but isn't installed here"_. Attempting to fix this by re-running claude plugin install for each missing plugin makes it worse — each fix wipes the entries installed before it.

What Should Happen?

claude plugin install should read the existing installed_plugins.json, merge the new plugin entry into the existing "plugins" object, and write the result back. All previously installed plugins should remain registered after installing a new one.

Error Messages/Logs

No explicit error is shown. The only observable signals are:

- The Plugins UI Errors tab shows N errors (one per project-scoped plugin, except the last-installed)
- Each error reads: `Plugin "X" is enabled in project settings but isn't installed here`
- Running `claude plugin install X --scope project` reports `✔ Successfully installed` but silently removes all other entries from the registry

Steps to Reproduce

1. Install two or more plugins at project scope sequentially:

``
claude plugin install plugin-a@marketplace --scope project
claude plugin install plugin-b@marketplace --scope project
``

1. Inspect ~/.claude/plugins/installed_plugins.json
2. Observe that only plugin-b is present — plugin-a's entry has been overwritten

Additional context: Discovered after brew upgrade claude to 2.1.195. Plugins installed before the upgrade were correctly present in installed_plugins.json. The overwrite behavior began with the first claude plugin install run after the upgrade.

Claude Model

Not sure / Multiple models

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

2.1.195 (Claude Code)

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

The plugin cache files under ~/.claude/plugins/cache/ are not affected — all plugin content is correctly downloaded. Only the installation registry (installed_plugins.json) is corrupted by the overwrite.

Workaround: Manually reconstruct ~/.claude/plugins/installed_plugins.json by merging all entries:

{
  "version": 2,
  "plugins": {
    "plugin-a@marketplace": [
      {
        "scope": "project",
        "installPath": "~/.claude/plugins/cache/marketplace/plugin-a/<version>",
        "version": "<version>",
        "installedAt": "<timestamp>",
        "lastUpdated": "<timestamp>",
        "gitCommitSha": "<sha>",
        "projectPath": "/path/to/project"
      }
    ],
    "plugin-b@marketplace": [ "..." ]
  }
}

Note: The direct consequence of this is installing skills only to see the older skills with errors, next. Trying to follow the instruction to reinstall the plugins via cli does not work, since installing one uninstall the others.