[BUG] plugin install / marketplace add silently clears sandbox.filesystem configuration

Description

Running claude plugin install or claude plugin marketplace add rewrites ~/.claude/settings.json and replaces the sandbox.filesystem object with {}, silently dropping the entire write.allowOnly configuration. This effectively disables the write sandbox without any warning.

Steps to Reproduce

1. Configure sandbox.filesystem.write.allowOnly in ~/.claude/settings.json
2. Run any plugin install command, e.g.:

• claude plugin install pyright-lsp@claude-plugins-official
• claude plugin marketplace add obra/superpowers-marketplace

1. Inspect ~/.claude/settings.json

Expected Behavior

sandbox.filesystem configuration is preserved after plugin operations.

Actual Behavior

The sandbox.filesystem key is replaced with {}, removing all write restrictions.

Before

"sandbox": {
  "enabled": true,
  "autoAllowBashIfSandboxed": true,
  "network": { ... },
  "filesystem": {
    "write": {
      "allowOnly": [
        "//root/code/**",
        "//tmp/**",
        "//tmp/claude-0/**"
      ]
    }
  }
}

After

"sandbox": {
  "enabled": true,
  "autoAllowBashIfSandboxed": true,
  "network": { ... },
  "filesystem": {}
}

Security Implication

The write sandbox is a security boundary. Silently clearing it means users who configured filesystem restrictions to limit where Claude can write are unknowingly left without those protections after installing a plugin. There is no warning or prompt — the configuration is simply dropped.

Environment

• Claude Code version: 2.1.63
• OS: Linux (also likely reproducible on macOS)
• All claude plugin install variants appear affected

Related Issues

• #2688 — reported the same root cause since v1.0.35 (settings rewrite on plugin install)
• #15339 — closed as duplicate, but the underlying issue persists

Workaround

Manually verify and restore sandbox.filesystem.write in settings.json after every plugin install.