Address LLM Wiki greptile feedback

packages/plugins/plugin-llm-wiki/src/manifest.ts

@@ -161,9 +161,9 @@ const manifest: PaperclipPluginManifestV1 = {
       adapterType: "claude_local",
       adapterPreference: ["claude_local", "codex_local", "gemini_local", "opencode_local", "cursor", "pi_local"],
       adapterConfig: {
-        dangerouslySkipPermissions: true,
-        dangerouslyBypassApprovalsAndSandbox: true,
-        sandbox: false,
+        dangerouslySkipPermissions: false,
+        dangerouslyBypassApprovalsAndSandbox: false,
+        sandbox: true,
         paperclipSkillSync: {
           desiredSkills: WIKI_MANAGED_SKILL_CANONICAL_KEYS
         }

packages/plugins/plugin-llm-wiki/src/ui/index.tsx

@@ -159,6 +159,7 @@ type ManagedSkill = {
   status: string;
   skillId?: string | null;
   resourceKey?: string | null;
+  defaultDrift?: { changedFiles: string[] } | null;
   skill?: {
     id?: string;
     name?: string;
@@ -4878,9 +4879,11 @@ function buildSkillHealthItems(skills: ManagedSkill[]): RoutineHealthItem[] {
   }
   return skills.map((skill) => ({
     label: skillLabel(skill),
-    ok: managedSkillIsReady(skill),
+    ok: managedSkillIsReady(skill) && !skill.defaultDrift?.changedFiles.length,
     detail: managedSkillIsReady(skill)
-      ? `${skillLabel(skill)} is installed in the company skill library.`
+      ? skill.defaultDrift?.changedFiles.length
+        ? `${skillLabel(skill)} differs from the plugin default: ${skill.defaultDrift.changedFiles.join(", ")}.`
+        : `${skillLabel(skill)} is installed in the company skill library.`
       : `${skillLabel(skill)} is not installed in the company skill library.`,
   }));
 }

packages/plugins/plugin-llm-wiki/src/wiki.ts

@@ -183,6 +183,7 @@ export type WikiSkillResource = {
   resourceKey: string;
   skill: PluginManagedSkillResolution["skill"];
   details: { name: string; key: string; description: string | null } | null;
+  defaultDrift?: { changedFiles: string[] } | null;
 };
 
 export type WikiResourceOption = {
@@ -1591,6 +1592,7 @@ function skillResource(resolved: PluginManagedSkillResolution): WikiSkillResourc
     resourceKey: resolved.resourceKey,
     skill: resolved.skill,
     details: skillDetails(resolved.skill),
+    defaultDrift: resolved.defaultDrift ?? null,
   };
 }
 

packages/plugins/plugin-llm-wiki/tests/plugin.spec.ts

@@ -668,9 +668,9 @@ describe("LLM Wiki plugin scaffold", () => {
     expect(manifest.agents?.[0]?.agentKey).toBe("wiki-maintainer");
     expect(manifest.agents?.[0]?.adapterType).toBe("claude_local");
     expect(manifest.agents?.[0]?.adapterConfig).toMatchObject({
-      dangerouslySkipPermissions: true,
-      dangerouslyBypassApprovalsAndSandbox: true,
-      sandbox: false,
+      dangerouslySkipPermissions: false,
+      dangerouslyBypassApprovalsAndSandbox: false,
+      sandbox: true,
     });
     expect(manifest.agents?.[0]?.instructions?.entryFile).toBe("AGENTS.md");
     expect(manifest.agents?.[0]?.instructions?.content).toContain("You are the maintainer of this personal wiki");
@@ -1137,6 +1137,29 @@ Duplicate headings receive stable suffixes.
     expect(markup).toContain("Re-sync skills");
   });
 
+  it("shows managed skill default drift in setup health", () => {
+    mockPathname = "/PAP/wiki/settings";
+    mockSettingsManagedSkills = [{
+      status: "resolved",
+      skillId: "skill-1",
+      resourceKey: WIKI_MAINTAINER_SKILL_KEY,
+      defaultDrift: { changedFiles: ["SKILL.md"] },
+      details: {
+        name: "LLM Wiki Maintainer",
+        key: WIKI_MAINTAINER_SKILL_CANONICAL_KEY,
+        description: null,
+      },
+    }];
+
+    const markup = renderToStaticMarkup(createElement(WikiPage, {
+      context: { companyId: COMPANY_ID, companyPrefix: "PAP" },
+    } as never));
+
+    expect(markup).toContain("skill issue(s) need attention");
+    expect(markup).toContain("LLM Wiki Maintainer differs from the plugin default: SKILL.md.");
+    expect(markup).toContain("Re-sync skills");
+  });
+
   it("renders host settings directly as the Setup page without an extra plugin heading", () => {
     const markup = renderToStaticMarkup(createElement(SettingsPage, {
       context: { companyId: COMPANY_ID, companyPrefix: "PAP" },

packages/shared/src/types/plugin.ts

@@ -321,6 +321,9 @@ export interface PluginManagedSkillResolution {
   skillId: string | null;
   skill: CompanySkill | null;
   status: "missing" | "resolved" | "created" | "relinked" | "reset";
+  defaultDrift?: {
+    changedFiles: string[];
+  } | null;
 }
 
 /**

server/src/__tests__/plugin-managed-skills.test.ts

@@ -174,6 +174,27 @@ describeEmbeddedPostgres("plugin-managed skills", () => {
     expect(reset.skill?.markdown).toContain("key: \"plugin/paperclip-managed-skills-test/wiki-maintainer\"");
   });
 
+  it("reports drift when installed skill files differ from plugin defaults", async () => {
+    const { companyId, services } = await seedCompanyAndPlugin();
+    const created = await services.skills.managedReconcile({ companyId, skillKey: "wiki-maintainer" });
+    expect(created.defaultDrift).toBeNull();
+
+    await db
+      .update(companySkills)
+      .set({
+        markdown: "# Custom instructions\n",
+        updatedAt: new Date(),
+      })
+      .where(eq(companySkills.id, created.skillId!));
+
+    const drifted = await services.skills.managedReconcile({ companyId, skillKey: "wiki-maintainer" });
+    expect(drifted.status).toBe("resolved");
+    expect(drifted.defaultDrift).toEqual({ changedFiles: ["SKILL.md"] });
+
+    const reset = await services.skills.managedReset({ companyId, skillKey: "wiki-maintainer" });
+    expect(reset.defaultDrift).toBeNull();
+  });
+
   it("adds the canonical managed key to manifest-provided markdown skills", async () => {
     const pluginManifest = manifest();
     pluginManifest.skills = [

server/src/services/plugin-managed-skills.ts

@@ -91,6 +91,20 @@ function buildPackageFiles(
   return files;
 }
 
+function buildDeclaredSkillFiles(
+  pluginKey: string,
+  declaration: PluginManagedSkillDeclaration,
+) {
+  const packageFiles = buildPackageFiles(pluginKey, declaration);
+  const root = declaration.skillKey;
+  const prefix = `${root}/`;
+  const files: Record<string, string> = {};
+  for (const [filePath, content] of Object.entries(packageFiles)) {
+    files[filePath.startsWith(prefix) ? filePath.slice(prefix.length) : filePath] = content;
+  }
+  return files;
+}
+
 function buildSkillDefaults(
   pluginKey: string,
   declaration: PluginManagedSkillDeclaration,
@@ -114,6 +128,7 @@ function resolution(
   declaration: PluginManagedSkillDeclaration,
   skill: CompanySkill | null,
   status: PluginManagedSkillResolution["status"],
+  defaultDrift: PluginManagedSkillResolution["defaultDrift"] = null,
 ): PluginManagedSkillResolution {
   return {
     pluginKey,
@@ -123,6 +138,7 @@ function resolution(
     skillId: skill?.id ?? null,
     skill,
     status,
+    defaultDrift,
   };
 }
 
@@ -191,6 +207,53 @@ export function pluginManagedSkillService(
     return skills.getById(companyId, skillId);
   }
 
+  async function managedSkillDefaultDrift(
+    companyId: string,
+    skill: CompanySkill | null,
+    declaration: PluginManagedSkillDeclaration,
+  ): Promise<PluginManagedSkillResolution["defaultDrift"]> {
+    if (!skill) return null;
+    const declaredFiles = buildDeclaredSkillFiles(options.pluginKey, declaration);
+    const currentFiles: Record<string, string | null> = {};
+    const paths = new Set([
+      ...Object.keys(declaredFiles),
+      ...skill.fileInventory.map((entry) => entry.path),
+    ]);
+
+    for (const filePath of paths) {
+      if (filePath === "SKILL.md") {
+        currentFiles[filePath] = skill.markdown;
+        continue;
+      }
+      try {
+        currentFiles[filePath] = (await skills.readFile(companyId, skill.id, filePath))?.content ?? null;
+      } catch {
+        currentFiles[filePath] = null;
+      }
+    }
+
+    const changedFiles = [...paths]
+      .filter((filePath) => (currentFiles[filePath] ?? null) !== (declaredFiles[filePath] ?? null))
+      .sort((left, right) => left.localeCompare(right));
+    return changedFiles.length > 0 ? { changedFiles } : null;
+  }
+
+  async function resolvedSkill(
+    companyId: string,
+    declaration: PluginManagedSkillDeclaration,
+    skill: CompanySkill | null,
+    status: PluginManagedSkillResolution["status"],
+  ) {
+    return resolution(
+      options.pluginKey,
+      companyId,
+      declaration,
+      skill,
+      status,
+      await managedSkillDefaultDrift(companyId, skill, declaration),
+    );
+  }
+
   async function importDeclaredSkill(
     companyId: string,
     declaration: PluginManagedSkillDeclaration,
@@ -224,9 +287,9 @@ export function pluginManagedSkillService(
   async function get(skillKey: string, companyId: string) {
     const declaration = declarationFor(skillKey);
     const binding = await getBinding(companyId, skillKey);
-    if (!binding) return resolution(options.pluginKey, companyId, declaration, null, "missing");
+    if (!binding) return resolvedSkill(companyId, declaration, null, "missing");
     const skill = await getSkill(companyId, binding.resourceId);
-    return resolution(options.pluginKey, companyId, declaration, skill, skill ? "resolved" : "missing");
+    return resolvedSkill(companyId, declaration, skill, skill ? "resolved" : "missing");
   }
 
   async function reconcile(skillKey: string, companyId: string) {
@@ -250,7 +313,7 @@ export function pluginManagedSkillService(
         status: imported.status,
       },
     });
-    return resolution(options.pluginKey, companyId, declaration, imported.skill, imported.status);
+    return resolvedSkill(companyId, declaration, imported.skill, imported.status);
   }
 
   async function reset(skillKey: string, companyId: string) {
@@ -268,7 +331,7 @@ export function pluginManagedSkillService(
         managedResourceKey: declaration.skillKey,
       },
     });
-    return resolution(options.pluginKey, companyId, declaration, imported.skill, "reset");
+    return resolvedSkill(companyId, declaration, imported.skill, "reset");
   }
 
   return {