fix(plugins): stop stripLegacyHooks from deleting the plugin's own hooks

claude plugin install materializes the plugin's inline hooks into
~/.claude/settings.json itself, with \${CLAUDE_PLUGIN_ROOT} resolved to the
actual cache path — confirmed by installing the plugin for real and
inspecting the file. Those entries also contain "hook-handler.js", so
isOurEntry()'s plain substring match could not tell a legitimate
plugin-installed hook from a leftover npm run install-hooks entry: every
SessionStart would have stripped the plugin's own working hooks right back
out. isCheckoutHookEntry() only removes entries whose command does NOT
resolve under ~/.claude/plugins/cache/. plugin-doctor.js's duplicate-hook
count uses the same predicate.

scripts/plugin-bootstrap.js

@@ -187,11 +187,37 @@ function releaseLock(rt = runtimeDir()) {
 
 /* --------------------------------------------------------- legacy cleanup */
 
+/**
+ * `claude plugin install` materializes the plugin's inline hooks into
+ * `~/.claude/settings.json` itself, with `${CLAUDE_PLUGIN_ROOT}` already
+ * resolved to the cache path — confirmed by installing this plugin for real
+ * and inspecting the file. Those entries also contain `hook-handler.js`, so
+ * `isOurEntry()` alone (checkout vs. plugin, both match the same substring)
+ * cannot tell a legitimate plugin-installed hook from a leftover
+ * `npm run install-hooks` entry. Only entries whose command does NOT resolve
+ * under the plugin cache are the legacy, checkout-installed kind.
+ *
+ * @returns {(entry: object) => boolean}
+ */
+function isCheckoutHookEntry(claudeHome = getClaudeHome()) {
+  const cacheRoot = path.join(claudeHome, "plugins", "cache");
+  return (entry) => {
+    if (!isOurEntry(entry)) return false;
+    const commands = [
+      entry.command,
+      ...(Array.isArray(entry.hooks) ? entry.hooks.map((h) => h.command) : []),
+    ];
+    return !commands.some((c) => typeof c === "string" && c.includes(cacheRoot));
+  };
+}
+
 /**
  * Remove hook entries a previous `npm run install-hooks` wrote into
  * ~/.claude/settings.json. The plugin installs its own hooks, and events carry
  * no id — two handlers mean every token and cost figure is counted twice.
- * The original file is copied aside before any write.
+ * Never touches the plugin's own cache-resolved entries (see
+ * `isCheckoutHookEntry`) — only genuine leftover checkout paths. The original
+ * file is copied aside before any write.
  *
  * @returns {number} how many entries were removed
  */
@@ -204,10 +230,11 @@ function stripLegacyHooks(settingsPath = getSettingsPath()) {
   }
   if (!settings.hooks || typeof settings.hooks !== "object") return 0;
 
+  const isLegacy = isCheckoutHookEntry();
   let removed = 0;
   for (const [type, entries] of Object.entries(settings.hooks)) {
     if (!Array.isArray(entries)) continue;
-    const kept = entries.filter((e) => !isOurEntry(e));
+    const kept = entries.filter((e) => !isLegacy(e));
     removed += entries.length - kept.length;
     if (kept.length) settings.hooks[type] = kept;
     else delete settings.hooks[type];
@@ -506,6 +533,7 @@ module.exports = {
   lockIsStale,
   acquireLock,
   releaseLock,
+  isCheckoutHookEntry,
   stripLegacyHooks,
   linkCli,
   installDeps,

scripts/plugin-doctor.js

@@ -14,7 +14,6 @@ const os = require("os");
 const path = require("path");
 
 const boot = require("./plugin-bootstrap");
-const { isOurEntry } = require("./install-hooks");
 const { getSettingsPath, getDataDir } = require("../server/lib/claude-home");
 const { mcpBuildStatus } = require("./check-mcp-build");
 
@@ -104,9 +103,10 @@ function countLegacyHookEntries() {
   try {
     const settings = JSON.parse(fs.readFileSync(getSettingsPath(), "utf8"));
     if (!settings.hooks) return 0;
+    const isLegacy = boot.isCheckoutHookEntry();
     return Object.values(settings.hooks)
       .filter(Array.isArray)
-      .reduce((n, entries) => n + entries.filter(isOurEntry).length, 0);
+      .reduce((n, entries) => n + entries.filter(isLegacy).length, 0);
   } catch {
     return 0;
   }