[BUG] Plugins and MCP servers become invisible after alternating between Claude Code CLI and Antigravity IDE (VS Code extension)

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?

After alternating between Claude Code CLI and the Antigravity IDE (VS Code extension) in the same project directory, all marketplace plugins become invisible in the Plugin UI — they don't appear in the "Installed" tab, yet the "Discover" tab also fails to show some of them (as if they're partially recognized as installed). MCP servers contributed by plugins stop loading entirely.

Key observations:

1. ~/.claude/plugins/installed_plugins.json correctly lists all 12 installed plugins with valid paths and versions — the registration data is intact.
2. Plugin cache files exist and are complete under ~/.claude/plugins/cache/claude-plugins-official/.
3. Skills from plugins survive because they are symlinked/copied into ~/.claude/skills/ and loaded independently of the plugin system.
4. MCP servers from plugins do NOT survive — /mcp returns "No MCP servers configured" even though .mcp.json files exist inside each plugin's cache directory.
5. The Plugin marketplace UI is in an inconsistent state:

• Some plugins (e.g., context7, figma) appear in "Installed" but only show an "MCP" badge, as if they are incomplete installations.
• Other plugins (e.g., frontend-design, superpowers) that were originally installed via the marketplace are not shown in "Installed" at all, despite their skills being active.
• Some of these "installed" plugins still appear in the "Discover" tab as if available for fresh installation.

What Should Happen?

1. Plugins registered in installed_plugins.json should be fully recognized by the Plugin UI regardless of whether another IDE was used in the same project directory.
2. MCP servers declared in plugin .mcp.json files should be loaded when the plugin is registered as installed.
3. The "Installed" tab should accurately reflect all plugins listed in installed_plugins.json.
4. The "Discover" tab should not show plugins that are already installed.

Error Messages/Logs

/mcp output:
No MCP servers configured. Please run /doctor if this is unexpected.
Otherwise, run `claude mcp --help` or visit https://code.claude.com/docs/en/mcp to learn more.

No error messages in the UI — plugins simply don't appear.

Steps to Reproduce

1. Install Claude Code CLI (v2.1.71) on Windows 11.
2. Install several plugins from the marketplace (e.g., context7, supabase, github, superpowers, frontend-design, playwright, figma, vercel, skill-creator, etc.).
3. Verify plugins are working: /mcp shows MCP servers, /skills shows plugin skills, "Installed" tab shows all plugins.
4. Open the same project directory in Antigravity IDE (Claude Code VS Code extension).
5. Optionally install some skills/plugins within Antigravity IDE (this creates an .agent/ directory with its own skill structure).
6. Close Antigravity IDE and relaunch Claude Code CLI.
7. Run /mcp — returns "No MCP servers configured".
8. Open Plugin marketplace — "Installed" tab is incomplete or empty; some plugins appear in "Discover" as if not installed.
9. Run /skills — skills from plugins still work (loaded from ~/.claude/skills/).
10. This persists across restarts. Restarting Claude Code does not fix the issue.

Investigation Details

Files examined:

• ~/.claude/plugins/installed_plugins.json — Contains all 12 plugins with correct installPath, version, gitCommitSha. Data is intact.
• ~/.claude/plugins/cache/claude-plugins-official/*/ — All plugin directories exist with complete contents (.claude-plugin/plugin.json, .mcp.json, skills/, etc.).
• ~/.claude.json — The mcpServers field at root level was empty {} before manual intervention. Project-level mcpServers under projects."D:/Projects/Level Up" was also {}.
• ~/.claude/settings.json — Does NOT support mcpServers (writing MCP config here has no effect).

Workarounds attempted:

1. Editing ~/.claude/settings.json to add mcpServers — No effect. Claude Code does not read MCP config from this file.
2. Creating .claude/settings/mcp.json at project level — No effect on /mcp output.
3. Using claude mcp add -s user CLI command — Successfully writes to ~/.claude.json mcpServers field, and MCP servers are recognized after restart. However, this is a manual workaround that bypasses the plugin system entirely.
4. Recreating symlinks from plugin skill directories to ~/.claude/skills/ — Skills were already working, but this confirmed the plugin loader is not creating these links automatically.

Root cause hypothesis:

The Antigravity IDE (VS Code extension) appears to modify or reset some runtime state or cache that the Claude Code CLI plugin loader depends on. The installed_plugins.json registration survives, but the plugin activation/loading pipeline is broken — it no longer reads .mcp.json from installed plugins or properly reports them in the UI.

This may be related to #29132 (MCP/plugins not persisting on Windows) and the non-atomic .claude.json write issue described there, where concurrent or alternating access from multiple Claude Code processes corrupts the config state.

Claude Model

Opus 4.6

Is this a regression?

Yes, this worked in a previous version

Last Working Version

Plugins were fully functional before using Antigravity IDE in the same project (approximately v2.1.62 timeframe).

Claude Code Version

2.1.71 (Claude Code)

Platform

Anthropic API

Operating System

Windows 11

Terminal/Shell

Git Bash

Additional Information

• Antigravity IDE creates its own .agent/skills/ directory structure in the project, which is separate from Claude Code's ~/.claude/skills/.
• The issue is reproducible: every time Antigravity IDE is opened in the same project directory and then Claude Code CLI is relaunched, the plugin state breaks again.
• User-level skills in ~/.claude/skills/ (both manually created and symlinked from plugins) continue to work correctly — only the plugin system's MCP loading and UI state are affected.