`claude plugin enable|disable --scope project` rewrites .claude/settings.json and empties `footerLinksRegexes`

**Version:** Claude Code 2.1.261, macOS (Darwin 27.0.0)

**What happens**

Running `claude plugin enable ` or `claude plugin disable ` with `--scope project` (or with no scope when the plugin is installed at project scope) rewrites the whole `.claude/settings.json`:

1. Keys are reordered (`statusLine`, `subagentStatusLine`, `enabledPlugins`, `footerLinksRegexes` move to the end).
2. `footerLinksRegexes` is replaced with an empty array `[]` every time, whatever it contained. Tested with `["graft/[\\w./-]+\\.md"]` and with the trivial `["graft/.*"]`; both come back as `[]`.
3. Unknown top-level keys survive (a probe key `"zzzProbe": 1` was kept), so this is specific to `footerLinksRegexes`, not a general schema strip.

**Expected**

Only `enabledPlugins` should change. Other keys and their order should be left as they were.

**Repro**

```sh
mkdir repro && cd repro && git init -q
mkdir .claude
cat > .claude/settings.json <<'EOF'
{
"footerLinksRegexes": ["graft/.*"],
"enabledPlugins": {}
}
EOF
claude plugin enable superpowers@claude-plugins-official --scope project
cat .claude/settings.json # footerLinksRegexes is now []
```

**Impact**

The `footerLinksRegexes` entry is written by the `@nanonets/graft` tool's `graft init` to make its footer links clickable. Any plugin toggle silently removes it in a checked-in file, so the breakage lands in the repo unnoticed unless someone diffs settings after a plugin command.

Reproduce the loss using the provided commands and inspect .claude/settings.json before and after a project-scope plugin toggle. Trace the settings rewrite triggered by `claude plugin enable|disable --scope project`, focusing on why footerLinksRegexes becomes an empty array. Done means only enabledPlugins changes while footerLinksRegexes, unknown keys, and existing ordering remain intact.

Written by the indexing model from the issue text.