Merge branch 'skill-pat-feature'

packages/shared/src/index.ts

@@ -557,6 +557,7 @@ export {
   companySkillDetailSchema,
   companySkillUpdateStatusSchema,
   companySkillImportSchema,
+  companySkillUpdateAuthSchema,
   companySkillProjectScanRequestSchema,
   companySkillProjectScanSkippedSchema,
   companySkillProjectScanConflictSchema,

packages/shared/src/validators/company-skill.ts

@@ -66,6 +66,11 @@ export const companySkillUpdateStatusSchema = z.object({
 
 export const companySkillImportSchema = z.object({
   source: z.string().min(1),
+  authToken: z.string().min(1).optional(),
+});
+
+export const companySkillUpdateAuthSchema = z.object({
+  authToken: z.string().min(1).nullable(),
 });
 
 export const companySkillProjectScanRequestSchema = z.object({
@@ -133,3 +138,4 @@ export type CompanySkillImport = z.infer<typeof companySkillImportSchema>;
 export type CompanySkillProjectScan = z.infer<typeof companySkillProjectScanRequestSchema>;
 export type CompanySkillCreate = z.infer<typeof companySkillCreateSchema>;
 export type CompanySkillFileUpdate = z.infer<typeof companySkillFileUpdateSchema>;
+export type CompanySkillUpdateAuth = z.infer<typeof companySkillUpdateAuthSchema>;

packages/shared/src/validators/index.ts

@@ -44,6 +44,7 @@ export {
   companySkillDetailSchema,
   companySkillUpdateStatusSchema,
   companySkillImportSchema,
+  companySkillUpdateAuthSchema,
   companySkillProjectScanRequestSchema,
   companySkillProjectScanSkippedSchema,
   companySkillProjectScanConflictSchema,
@@ -55,6 +56,7 @@ export {
   type CompanySkillProjectScan,
   type CompanySkillCreate,
   type CompanySkillFileUpdate,
+  type CompanySkillUpdateAuth,
 } from "./company-skill.js";
 export {
   agentSkillStateSchema,

server/src/__tests__/company-skills-routes.test.ts

@@ -89,6 +89,7 @@ describe("company skill mutation permissions", () => {
     expect(mockCompanySkillService.importFromSource).toHaveBeenCalledWith(
       "company-1",
       "https://github.com/vercel-labs/agent-browser",
+      undefined,
     );
   });
 
@@ -266,6 +267,7 @@ describe("company skill mutation permissions", () => {
     expect(mockCompanySkillService.importFromSource).toHaveBeenCalledWith(
       "company-1",
       "https://github.com/vercel-labs/agent-browser",
+      undefined,
     );
   });
 

server/src/routes/company-skills.ts

@@ -4,6 +4,7 @@ import {
   companySkillCreateSchema,
   companySkillFileUpdateSchema,
   companySkillImportSchema,
+  companySkillUpdateAuthSchema,
   companySkillProjectScanRequestSchema,
 } from "@paperclipai/shared";
 import { trackSkillImported } from "@paperclipai/shared/telemetry";
@@ -194,7 +195,8 @@ export function companySkillRoutes(db: Db) {
       const companyId = req.params.companyId as string;
       await assertCanMutateCompanySkills(req, companyId);
       const source = String(req.body.source ?? "");
-      const result = await svc.importFromSource(companyId, source);
+      const authToken = typeof req.body.authToken === "string" ? req.body.authToken.trim() : undefined;
+      const result = await svc.importFromSource(companyId, source, authToken || undefined);
 
       const actor = getActorInfo(req);
       await logActivity(db, {
@@ -260,6 +262,36 @@ export function companySkillRoutes(db: Db) {
     },
   );
 
+  router.delete("/companies/:companyId/skills/by-source", async (req, res) => {
+    const companyId = req.params.companyId as string;
+    const sourceLocator = String(req.query.source ?? "").trim();
+    if (!sourceLocator) {
+      res.status(400).json({ error: "source query parameter is required" });
+      return;
+    }
+    await assertCanMutateCompanySkills(req, companyId);
+    const deleted = await svc.deleteBySource(companyId, sourceLocator);
+
+    const actor = getActorInfo(req);
+    await logActivity(db, {
+      companyId,
+      actorType: actor.actorType,
+      actorId: actor.actorId,
+      agentId: actor.agentId,
+      runId: actor.runId,
+      action: "company.skills_source_deleted",
+      entityType: "company",
+      entityId: companyId,
+      details: {
+        sourceLocator,
+        deletedCount: deleted.length,
+        deletedSlugs: deleted.map((s) => s.slug),
+      },
+    });
+
+    res.json({ deleted });
+  });
+
   router.delete("/companies/:companyId/skills/:skillId", async (req, res) => {
     const companyId = req.params.companyId as string;
     const skillId = req.params.skillId as string;
@@ -318,5 +350,38 @@ export function companySkillRoutes(db: Db) {
     res.json(result);
   });
 
+  router.patch(
+    "/companies/:companyId/skills/:skillId/auth",
+    validate(companySkillUpdateAuthSchema),
+    async (req, res) => {
+      const companyId = req.params.companyId as string;
+      const skillId = req.params.skillId as string;
+      await assertCanMutateCompanySkills(req, companyId);
+      const authToken = req.body.authToken as string | null;
+      const result = await svc.updateSkillAuth(companyId, skillId, authToken);
+      if (!result) {
+        res.status(404).json({ error: "Skill not found" });
+        return;
+      }
+
+      const actor = getActorInfo(req);
+      await logActivity(db, {
+        companyId,
+        actorType: actor.actorType,
+        actorId: actor.actorId,
+        agentId: actor.agentId,
+        runId: actor.runId,
+        action: authToken ? "company.skill_auth_updated" : "company.skill_auth_removed",
+        entityType: "company_skill",
+        entityId: result.id,
+        details: {
+          slug: result.slug,
+        },
+      });
+
+      res.json(result);
+    },
+  );
+
   return router;
 }

server/src/services/company-skills.ts

@@ -471,20 +471,20 @@ function parseFrontmatterMarkdown(raw: string): { frontmatter: Record<string, un
   };
 }
 
-async function fetchText(url: string) {
+async function fetchText(url: string, authToken?: string) {
-  const response = await ghFetch(url);
+  const response = await ghFetch(url, undefined, authToken);
   if (!response.ok) {
     throw unprocessable(`Failed to fetch ${url}: ${response.status}`);
   }
   return response.text();
 }
 
-async function fetchJson<T>(url: string): Promise<T> {
+async function fetchJson<T>(url: string, authToken?: string): Promise<T> {
   const response = await ghFetch(url, {
     headers: {
       accept: "application/vnd.github+json",
     },
-  });
+  }, authToken);
   if (!response.ok) {
     throw unprocessable(`Failed to fetch ${url}: ${response.status}`);
   }
@@ -492,16 +492,18 @@ async function fetchJson<T>(url: string): Promise<T> {
 }
 
 
-async function resolveGitHubDefaultBranch(owner: string, repo: string, apiBase: string) {
+async function resolveGitHubDefaultBranch(owner: string, repo: string, apiBase: string, authToken?: string) {
   const response = await fetchJson<{ default_branch?: string }>(
     `${apiBase}/repos/${owner}/${repo}`,
+    authToken,
   );
   return asString(response.default_branch) ?? "main";
 }
 
-async function resolveGitHubCommitSha(owner: string, repo: string, ref: string, apiBase: string) {
+async function resolveGitHubCommitSha(owner: string, repo: string, ref: string, apiBase: string, authToken?: string) {
   const response = await fetchJson<{ sha?: string }>(
     `${apiBase}/repos/${owner}/${repo}/commits/${encodeURIComponent(ref)}`,
+    authToken,
   );
   const sha = asString(response.sha);
   if (!sha) {
@@ -538,7 +540,7 @@ function parseGitHubSourceUrl(rawUrl: string) {
   return { hostname: url.hostname, owner, repo, ref, basePath, filePath, explicitRef };
 }
 
-async function resolveGitHubPinnedRef(parsed: ReturnType<typeof parseGitHubSourceUrl>) {
+async function resolveGitHubPinnedRef(parsed: ReturnType<typeof parseGitHubSourceUrl>, authToken?: string) {
   const apiBase = gitHubApiBase(parsed.hostname);
   if (/^[0-9a-f]{40}$/i.test(parsed.ref.trim())) {
     return {
@@ -549,8 +551,8 @@ async function resolveGitHubPinnedRef(parsed: ReturnType<typeof parseGitHubSourc
 
   const trackingRef = parsed.explicitRef
     ? parsed.ref
-    : await resolveGitHubDefaultBranch(parsed.owner, parsed.repo, apiBase);
+    : await resolveGitHubDefaultBranch(parsed.owner, parsed.repo, apiBase, authToken);
-  const pinnedRef = await resolveGitHubCommitSha(parsed.owner, parsed.repo, trackingRef, apiBase);
+  const pinnedRef = await resolveGitHubCommitSha(parsed.owner, parsed.repo, trackingRef, apiBase, authToken);
   return { pinnedRef, trackingRef };
 }
 
@@ -981,6 +983,7 @@ async function readUrlSkillImports(
   companyId: string,
   sourceUrl: string,
   requestedSkillSlug: string | null = null,
+  authToken?: string,
 ): Promise<{ skills: ImportedSkill[]; warnings: string[] }> {
   const url = sourceUrl.trim();
   const warnings: string[] = [];
@@ -995,10 +998,11 @@ async function readUrlSkillImports(
   if (looksLikeRepoUrl) {
     const parsed = parseGitHubSourceUrl(url);
     const apiBase = gitHubApiBase(parsed.hostname);
-    const { pinnedRef, trackingRef } = await resolveGitHubPinnedRef(parsed);
+    const { pinnedRef, trackingRef } = await resolveGitHubPinnedRef(parsed, authToken);
     let ref = pinnedRef;
     const tree = await fetchJson<{ tree?: Array<{ path: string; type: string }> }>(
       `${apiBase}/repos/${parsed.owner}/${parsed.repo}/git/trees/${ref}?recursive=1`,
+      authToken,
     ).catch(() => {
       throw unprocessable(`Failed to read GitHub tree for ${url}`);
     });
@@ -1025,7 +1029,7 @@ async function readUrlSkillImports(
     const skills: ImportedSkill[] = [];
     for (const relativeSkillPath of skillPaths) {
       const repoSkillPath = basePrefix ? `${basePrefix}${relativeSkillPath}` : relativeSkillPath;
-      const markdown = await fetchText(resolveRawGitHubUrl(parsed.hostname, parsed.owner, parsed.repo, ref, repoSkillPath));
+      const markdown = await fetchText(resolveRawGitHubUrl(parsed.hostname, parsed.owner, parsed.repo, ref, repoSkillPath), authToken);
       const parsedMarkdown = parseFrontmatterMarkdown(markdown);
       const skillDir = path.posix.dirname(relativeSkillPath);
       const slug = deriveImportedSkillSlug(parsedMarkdown.frontmatter, path.posix.basename(skillDir));
@@ -1087,7 +1091,7 @@ async function readUrlSkillImports(
   }
 
   if (url.startsWith("http://") || url.startsWith("https://")) {
-    const markdown = await fetchText(url);
+    const markdown = await fetchText(url, authToken);
     const parsedMarkdown = parseFrontmatterMarkdown(markdown);
     const urlObj = new URL(url);
     const fileName = path.posix.basename(urlObj.pathname);
@@ -1459,6 +1463,22 @@ export function companySkillService(db: Db) {
   const projects = projectService(db);
   const secretsSvc = secretService(db);
 
+  /** Resolve the GitHub auth token from a skill's metadata, if stored. */
+  async function resolveSkillAuthToken(
+    companyId: string,
+    skill: { metadata: Record<string, unknown> | null },
+  ): Promise<string | undefined> {
+    const meta = skill.metadata;
+    if (!meta) return undefined;
+    const secretId = typeof meta.sourceAuthSecretId === "string" ? meta.sourceAuthSecretId.trim() : "";
+    if (!secretId) return undefined;
+    try {
+      return await secretsSvc.resolveSecretValue(companyId, secretId, "latest");
+    } catch {
+      return undefined;
+    }
+  }
+
   async function ensureBundledSkills(companyId: string) {
     for (const skillsRoot of resolveBundledSkillsRoot()) {
       const stats = await fs.stat(skillsRoot).catch(() => null);
@@ -1656,7 +1676,8 @@ export function companySkillService(db: Db) {
 
     const hostname = asString(metadata.hostname) || "github.com";
     const apiBase = gitHubApiBase(hostname);
-    const latestRef = await resolveGitHubCommitSha(owner, repo, trackingRef, apiBase);
+    const authToken = await resolveSkillAuthToken(companyId, skill);
+    const latestRef = await resolveGitHubCommitSha(owner, repo, trackingRef, apiBase, authToken);
     return {
       supported: true,
       reason: null,
@@ -1700,8 +1721,9 @@ export function companySkillService(db: Db) {
       if (!owner || !repo) {
         throw unprocessable("Skill source metadata is incomplete.");
       }
+      const authToken = await resolveSkillAuthToken(companyId, skill);
       const repoPath = normalizePortablePath(path.posix.join(repoSkillDir, normalizedPath));
-      content = await fetchText(resolveRawGitHubUrl(hostname, owner, repo, ref, repoPath));
+      content = await fetchText(resolveRawGitHubUrl(hostname, owner, repo, ref, repoPath), authToken);
     } else if (skill.sourceType === "url") {
       if (normalizedPath !== "SKILL.md") {
         throw notFound("This skill source only exposes SKILL.md");
@@ -1818,7 +1840,8 @@ export function companySkillService(db: Db) {
       throw unprocessable("Skill source locator is missing.");
     }
 
-    const result = await readUrlSkillImports(companyId, skill.sourceLocator, skill.slug);
+    const authToken = await resolveSkillAuthToken(companyId, skill);
+    const result = await readUrlSkillImports(companyId, skill.sourceLocator, skill.slug, authToken);
     const matching = result.skills.find((entry) => entry.key === skill.key) ?? result.skills[0] ?? null;
     if (!matching) {
       throw unprocessable(`Skill ${skill.key} could not be re-imported from its source.`);
@@ -2230,6 +2253,10 @@ export function companySkillService(db: Db) {
       const metadata = {
         ...(skill.metadata ?? {}),
         skillKey: skill.key,
+        // Preserve auth secret reference across re-imports/updates
+        ...(existing?.metadata && typeof (existing.metadata as Record<string, unknown>).sourceAuthSecretId === "string"
+          ? { sourceAuthSecretId: (existing.metadata as Record<string, unknown>).sourceAuthSecretId }
+          : {}),
       };
       const values = {
         companyId,
@@ -2265,7 +2292,7 @@ export function companySkillService(db: Db) {
     return out;
   }
 
-  async function importFromSource(companyId: string, source: string): Promise<CompanySkillImportResult> {
+  async function importFromSource(companyId: string, source: string, authToken?: string): Promise<CompanySkillImportResult> {
     await ensureSkillInventoryCurrent(companyId);
     const parsed = parseSkillImportSourceInput(source);
     const local = !/^https?:\/\//i.test(parsed.resolvedSource);
@@ -2275,7 +2302,7 @@ export function companySkillService(db: Db) {
           .filter((skill) => !parsed.requestedSkillSlug || skill.slug === parsed.requestedSkillSlug),
         warnings: parsed.warnings,
       }
-      : await readUrlSkillImports(companyId, parsed.resolvedSource, parsed.requestedSkillSlug)
+      : await readUrlSkillImports(companyId, parsed.resolvedSource, parsed.requestedSkillSlug, authToken)
         .then((result) => ({
           skills: result.skills,
           warnings: [...parsed.warnings, ...result.warnings],
@@ -2302,6 +2329,35 @@ export function companySkillService(db: Db) {
       }
     }
     const imported = await upsertImportedSkills(companyId, filteredSkills);
+
+    // Store the auth token as an encrypted company secret and link to imported skills
+    if (authToken && imported.length > 0) {
+      for (const skill of imported) {
+        const secretName = `skill-pat:${skill.id}`;
+        let secretId: string;
+        const existing = await secretsSvc.getByName(companyId, secretName);
+        if (existing) {
+          await secretsSvc.rotate(existing.id, { value: authToken });
+          secretId = existing.id;
+        } else {
+          const created = await secretsSvc.create(companyId, {
+            name: secretName,
+            provider: "local_encrypted",
+            value: authToken,
+            description: `GitHub PAT for skill ${skill.slug}`,
+          });
+          secretId = created.id;
+        }
+        // Store the secret ID in skill metadata
+        const meta = (skill.metadata ?? {}) as Record<string, unknown>;
+        meta.sourceAuthSecretId = secretId;
+        await db
+          .update(companySkills)
+          .set({ metadata: meta, updatedAt: new Date() })
+          .where(and(eq(companySkills.id, skill.id), eq(companySkills.companyId, companyId)));
+      }
+    }
+
     return { imported, warnings };
   }
 
@@ -2341,9 +2397,104 @@ export function companySkillService(db: Db) {
     // Clean up materialized runtime files
     await fs.rm(resolveRuntimeSkillMaterializedPath(companyId, skill), { recursive: true, force: true });
 
+    // Delete associated PAT secret if present
+    const meta = skill.metadata as Record<string, unknown> | null;
+    const secretId = typeof meta?.sourceAuthSecretId === "string" ? meta.sourceAuthSecretId : null;
+    if (secretId) {
+      try {
+        await secretsSvc.remove(secretId);
+      } catch {
+        // Best-effort: don't fail the skill deletion if secret cleanup fails
+      }
+    }
+
     return skill;
   }
 
+  async function updateSkillAuth(
+    companyId: string,
+    skillId: string,
+    authToken: string | null,
+  ): Promise<CompanySkill | null> {
+    const skill = await getById(skillId);
+    if (!skill || skill.companyId !== companyId) return null;
+
+    const meta = (skill.metadata ?? {}) as Record<string, unknown>;
+    const existingSecretId = typeof meta.sourceAuthSecretId === "string" ? meta.sourceAuthSecretId : null;
+
+    if (authToken) {
+      // Set or update the PAT
+      const secretName = `skill-pat:${skill.id}`;
+      let secretId: string;
+      // Check metadata reference first, then fall back to name lookup
+      // (metadata ref may have been lost during a skill update/re-import)
+      const existingSecret = existingSecretId
+        ? await secretsSvc.getById(existingSecretId)
+        : await secretsSvc.getByName(companyId, secretName);
+      if (existingSecret) {
+        await secretsSvc.rotate(existingSecret.id, { value: authToken });
+        secretId = existingSecret.id;
+      } else {
+        const created = await secretsSvc.create(companyId, {
+          name: secretName,
+          provider: "local_encrypted",
+          value: authToken,
+          description: `GitHub PAT for skill ${skill.slug}`,
+        });
+        secretId = created.id;
+      }
+      meta.sourceAuthSecretId = secretId;
+    } else {
+      // Clear the PAT
+      delete meta.sourceAuthSecretId;
+      // Note: we don't delete the secret itself — it may be referenced in audit logs
+    }
+
+    const [updated] = await db
+      .update(companySkills)
+      .set({ metadata: meta, updatedAt: new Date() })
+      .where(and(eq(companySkills.id, skillId), eq(companySkills.companyId, companyId)))
+      .returning();
+    return updated ? toCompanySkill(updated) : null;
+  }
+
+  async function deleteBySource(companyId: string, sourceLocator: string): Promise<CompanySkill[]> {
+    const rows = await db
+      .select()
+      .from(companySkills)
+      .where(and(eq(companySkills.companyId, companyId), eq(companySkills.sourceLocator, sourceLocator)));
+    if (rows.length === 0) return [];
+
+    // Pre-check all skills for agent usage before deleting any (atomicity)
+    const skills = rows.map(toCompanySkill);
+    for (const skill of skills) {
+      const usedByAgents = await usage(companyId, skill.key);
+      if (usedByAgents.length > 0) {
+        const agentNames = usedByAgents.map((agent) => agent.name).sort((left, right) => left.localeCompare(right));
+        throw unprocessable(
+          `Cannot delete skills from "${sourceLocator}" because skill "${skill.name}" is still used by ${agentNames.join(", ")}. Detach it from those agents first.`,
+          {
+            skillId: skill.id,
+            skillKey: skill.key,
+            usedByAgents: usedByAgents.map((agent) => ({
+              id: agent.id,
+              name: agent.name,
+              urlKey: agent.urlKey,
+              adapterType: agent.adapterType,
+            })),
+          },
+        );
+      }
+    }
+
+    const deleted: CompanySkill[] = [];
+    for (const row of rows) {
+      const result = await deleteSkill(companyId, row.id);
+      if (result) deleted.push(result);
+    }
+    return deleted;
+  }
+
   return {
     list,
     listFull,
@@ -2359,7 +2510,9 @@ export function companySkillService(db: Db) {
     updateFile,
     createLocalSkill,
     deleteSkill,
+    deleteBySource,
     importFromSource,
+    updateSkillAuth,
     scanProjectWorkspaces,
     importPackageFiles,
     installUpdate,

server/src/services/github-fetch.ts

@@ -16,9 +16,13 @@ export function resolveRawGitHubUrl(hostname: string, owner: string, repo: strin
     : `https://${hostname}/raw/${owner}/${repo}/${ref}/${p}`;
 }
 
-export async function ghFetch(url: string, init?: RequestInit): Promise<Response> {
+export async function ghFetch(url: string, init?: RequestInit, authToken?: string): Promise<Response> {
+  const headers = new Headers(init?.headers);
+  if (authToken) {
+    headers.set("Authorization", `Bearer ${authToken}`);
+  }
   try {
-    return await fetch(url, init);
+    return await fetch(url, { ...init, headers });
   } catch {
     throw unprocessable(`Could not connect to ${new URL(url).hostname} — ensure the URL points to a GitHub or GitHub Enterprise instance`);
   }

ui/src/api/companySkills.ts

@@ -36,10 +36,23 @@ export const companySkillsApi = {
       `/companies/${encodeURIComponent(companyId)}/skills`,
       payload,
     ),
-  importFromSource: (companyId: string, source: string) =>
+  importFromSource: (companyId: string, source: string, authToken?: string) =>
     api.post<CompanySkillImportResult>(
       `/companies/${encodeURIComponent(companyId)}/skills/import`,
-      { source },
+      { source, ...(authToken ? { authToken } : {}) },
+    ),
+  updateAuth: (companyId: string, skillId: string, authToken: string | null) =>
+    api.patch<CompanySkill>(
+      `/companies/${encodeURIComponent(companyId)}/skills/${encodeURIComponent(skillId)}/auth`,
+      { authToken },
+    ),
+  remove: (companyId: string, skillId: string) =>
+    api.delete<CompanySkill>(
+      `/companies/${encodeURIComponent(companyId)}/skills/${encodeURIComponent(skillId)}`,
+    ),
+  removeBySource: (companyId: string, sourceLocator: string) =>
+    api.delete<{ deleted: CompanySkill[] }>(
+      `/companies/${encodeURIComponent(companyId)}/skills/by-source?source=${encodeURIComponent(sourceLocator)}`,
     ),
   scanProjects: (companyId: string, payload: CompanySkillProjectScanRequest = {}) =>
     api.post<CompanySkillProjectScanResult>(
@@ -51,8 +64,4 @@ export const companySkillsApi = {
       `/companies/${encodeURIComponent(companyId)}/skills/${encodeURIComponent(skillId)}/install-update`,
       {},
     ),
-  delete: (companyId: string, skillId: string) =>
-    api.delete<CompanySkill>(
-      `/companies/${encodeURIComponent(companyId)}/skills/${encodeURIComponent(skillId)}`,
-    ),
 };

ui/src/pages/CompanySkills.tsx

@@ -2,6 +2,7 @@ import { useEffect, useMemo, useState, type SVGProps } from "react";
 import { Link, useNavigate, useParams } from "@/lib/router";
 import { useMutation, useQuery, useQueryClient } from "@tanstack/react-query";
 import type {
+  CompanySkill,
   CompanySkillCreateRequest,
   CompanySkillDetail,
   CompanySkillFileDetail,
@@ -52,6 +53,7 @@ import {
   RefreshCw,
   Save,
   Search,
+  ShieldCheck,
   Trash2,
 } from "lucide-react";
 
@@ -487,6 +489,103 @@ function SkillList({
   );
 }
 
+function SkillAuthSection({
+  companyId,
+  skillId,
+  hasAuth,
+}: {
+  companyId: string;
+  skillId: string;
+  hasAuth: boolean;
+}) {
+  const queryClient = useQueryClient();
+  const { pushToast } = useToast();
+  const [editing, setEditing] = useState(false);
+  const [token, setToken] = useState("");
+
+  const updateAuth = useMutation({
+    mutationFn: (authToken: string | null) =>
+      companySkillsApi.updateAuth(companyId, skillId, authToken),
+    onSuccess: async () => {
+      await queryClient.invalidateQueries({ queryKey: queryKeys.companySkills.detail(companyId, skillId) });
+      setEditing(false);
+      setToken("");
+      pushToast({ tone: "success", title: "Auth updated" });
+    },
+    onError: (error) => {
+      pushToast({
+        tone: "error",
+        title: "Failed to update auth",
+        body: error instanceof Error ? error.message : "Unknown error",
+      });
+    },
+  });
+
+  return (
+    <div className="flex flex-wrap items-center gap-2">
+      <span className="text-[11px] uppercase tracking-[0.18em] text-muted-foreground">Auth</span>
+      {!editing ? (
+        <>
+          {hasAuth ? (
+            <>
+              <Button
+                variant="ghost"
+                size="sm"
+                onClick={() => setEditing(true)}
+              >
+                <ShieldCheck className="mr-1.5 h-3.5 w-3.5" />
+                PAT configured
+              </Button>
+              <button
+                className="inline-flex items-center text-muted-foreground/50 hover:text-destructive transition-colors"
+                onClick={() => updateAuth.mutate(null)}
+                disabled={updateAuth.isPending}
+                title="Remove PAT"
+              >
+                <Trash2 className="h-3.5 w-3.5" />
+              </button>
+            </>
+          ) : (
+            <Button
+              variant="ghost"
+              size="sm"
+              onClick={() => setEditing(true)}
+            >
+              Add PAT
+            </Button>
+          )}
+        </>
+      ) : (
+        <>
+          <input
+            type="password"
+            value={token}
+            onChange={(e) => setToken(e.target.value)}
+            placeholder="GitHub Personal Access Token"
+            className="flex-1 min-w-[200px] rounded-md border border-border px-2 py-1 bg-transparent text-xs outline-none placeholder:text-muted-foreground/50"
+            autoComplete="off"
+            autoFocus
+          />
+          <Button
+            size="sm"
+            onClick={() => updateAuth.mutate(token.trim())}
+            disabled={!token.trim() || updateAuth.isPending}
+          >
+            {updateAuth.isPending ? "Saving..." : "Save"}
+          </Button>
+          <Button
+            variant="ghost"
+            size="sm"
+            onClick={() => { setEditing(false); setToken(""); }}
+          >
+            Cancel
+          </Button>
+        </>
+      )}
+    </div>
+  );
+}
+
 function SkillPane({
   loading,
   detail,
@@ -525,7 +624,7 @@ function SkillPane({
   checkUpdatesPending: boolean;
   onInstallUpdate: () => void;
   installUpdatePending: boolean;
-  onDelete: () => void;
+  onDelete: (sourceLocator?: string | null) => void;
   deletePending: boolean;
   onSave: () => void;
   savePending: boolean;
@@ -572,7 +671,7 @@ function SkillPane({
             <Button
               variant="ghost"
               size="sm"
-              onClick={onDelete}
+              onClick={() => onDelete()}
               disabled={deletePending}
               title={removeDisabledReason ?? undefined}
             >
@@ -612,8 +711,23 @@ function SkillPane({
                 ) : (
                   <span className="truncate">{source.label}</span>
                 )}
+                <button
+                  className="inline-flex items-center text-muted-foreground/50 hover:text-destructive transition-colors"
+                  onClick={() => onDelete(detail.sourceLocator)}
+                  disabled={deletePending}
+                  title={detail.sourceLocator ? "Remove this source and all its skills" : "Remove this skill"}
+                >
+                  <Trash2 className="h-3.5 w-3.5" />
+                </button>
               </span>
             </div>
+            {(detail.sourceType === "github" || detail.sourceType === "skills_sh") && (
+              <SkillAuthSection
+                companyId={detail.companyId}
+                skillId={detail.id}
+                hasAuth={Boolean((detail.metadata as Record<string, unknown> | null)?.sourceAuthSecretId)}
+              />
+            )}
             {detail.sourceType === "github" && (
               <div className="flex flex-wrap items-center gap-2">
                 <span className="text-[11px] uppercase tracking-[0.18em] text-muted-foreground">Pin</span>
@@ -762,6 +876,7 @@ export function CompanySkills() {
   const { pushToast } = useToast();
   const [skillFilter, setSkillFilter] = useState("");
   const [source, setSource] = useState("");
+  const [importAuthToken, setImportAuthToken] = useState("");
   const [createOpen, setCreateOpen] = useState(false);
   const [emptySourceHelpOpen, setEmptySourceHelpOpen] = useState(false);
   const [expandedSkillId, setExpandedSkillId] = useState<string | null>(null);
@@ -775,6 +890,7 @@ export function CompanySkills() {
   const [deleteOpen, setDeleteOpen] = useState(false);
   const [deleteTargetSkillId, setDeleteTargetSkillId] = useState<string | null>(null);
   const [deleteTargetDetail, setDeleteTargetDetail] = useState<CompanySkillDetail | null>(null);
+  const [deleteTargetSourceLocator, setDeleteTargetSourceLocator] = useState<string | null>(null);
   const parsedRoute = useMemo(() => parseSkillRoute(routePath), [routePath]);
   const routeSkillId = parsedRoute.skillId;
   const selectedPath = parsedRoute.filePath;
@@ -883,11 +999,24 @@ export function CompanySkills() {
     if (!open) {
       setDeleteTargetSkillId(null);
       setDeleteTargetDetail(null);
+      setDeleteTargetSourceLocator(null);
+    }
+  }
+
+  function handleDeleteSkill(sourceLocator?: string | null) {
+    if (sourceLocator) {
+      setDeleteTargetSourceLocator(sourceLocator);
+      setDeleteTargetSkillId(null);
+      setDeleteTargetDetail(null);
+      setDeleteOpen(true);
+    } else {
+      openDeleteDialog();
     }
   }
 
   const importSkill = useMutation({
-    mutationFn: (importSource: string) => companySkillsApi.importFromSource(selectedCompanyId!, importSource),
+    mutationFn: ({ importSource, authToken }: { importSource: string; authToken?: string }) =>
+      companySkillsApi.importFromSource(selectedCompanyId!, importSource, authToken),
     onSuccess: async (result) => {
       await queryClient.invalidateQueries({ queryKey: queryKeys.companySkills.list(selectedCompanyId!) });
       if (result.imported[0]) navigate(skillRoute(result.imported[0].id));
@@ -900,6 +1029,7 @@ export function CompanySkills() {
         pushToast({ tone: "warn", title: "Import warnings", body: result.warnings[0] });
       }
       setSource("");
+      setImportAuthToken("");
     },
     onError: (error) => {
       pushToast({
@@ -1026,8 +1156,13 @@ export function CompanySkills() {
   });
 
   const deleteSkill = useMutation({
-    mutationFn: () => companySkillsApi.delete(selectedCompanyId!, deleteTargetSkillId!),
+    mutationFn: (sourceLocator?: string | null): Promise<{ deleted: CompanySkill[] }> => {
-    onSuccess: async (skill) => {
+      if (sourceLocator) {
+        return companySkillsApi.removeBySource(selectedCompanyId!, sourceLocator);
+      }
+      return companySkillsApi.remove(selectedCompanyId!, deleteTargetSkillId!).then((skill) => ({ deleted: [skill] }));
+    },
+    onSuccess: async (result) => {
       closeDeleteDialog(false);
       setDisplayedDetail(null);
       setDisplayedFile(null);
@@ -1048,10 +1183,10 @@ export function CompanySkills() {
         type: "active",
       });
       navigate("/skills", { replace: true });
+      const count = result.deleted.length;
       pushToast({
         tone: "success",
-        title: "Skill removed",
+        title: `${count} skill${count === 1 ? "" : "s"} removed`,
-        body: `${skill.name} was removed from the company skill library.`,
       });
     },
     onError: (error) => {
@@ -1073,7 +1208,8 @@ export function CompanySkills() {
       setEmptySourceHelpOpen(true);
       return;
     }
-    importSkill.mutate(trimmedSource);
+    const token = importAuthToken.trim() || undefined;
+    importSkill.mutate({ importSource: trimmedSource, authToken: token });
   }
 
   return (
@@ -1081,30 +1217,40 @@ export function CompanySkills() {
       <Dialog open={deleteOpen} onOpenChange={closeDeleteDialog}>
         <DialogContent className="sm:max-w-md">
           <DialogHeader>
-            <DialogTitle>Remove skill</DialogTitle>
+            <DialogTitle>{deleteTargetSourceLocator ? "Remove skills from source" : "Remove skill"}</DialogTitle>
             <DialogDescription>
-              Remove this skill from the company library. If any agents still use it, removal will be blocked until it is detached.
+              {deleteTargetSourceLocator
+                ? `All skills imported from this source will be permanently removed from the company library.`
+                : "Remove this skill from the company library. If any agents still use it, removal will be blocked until it is detached."}
             </DialogDescription>
           </DialogHeader>
           <div className="space-y-3 text-sm">
-            <p>
+            {deleteTargetSourceLocator ? (
-              {deleteTargetDetail
+              <p className="rounded-md border border-destructive/50 bg-destructive/5 px-3 py-2 font-mono text-xs break-all">
-                ? `You are about to remove ${deleteTargetDetail.name}.`
+                {deleteTargetSourceLocator}
-                : "You are about to remove this skill."}
-            </p>
-            {deleteTargetDetail?.usedByAgents?.length ? (
-              <div className="rounded-md border border-border px-3 py-3 text-muted-foreground">
-                Currently used by {deleteTargetDetail.usedByAgents.map((agent) => agent.name).join(", ")}.
-              </div>
-            ) : null}
-            {(deleteTargetDetail?.usedByAgents.length ?? 0) > 0 ? (
-              <p className="text-muted-foreground">
-                Detach this skill from all agents to enable removal.
               </p>
-            ) : null}
+            ) : (
+              <>
+                <p>
+                  {deleteTargetDetail
+                    ? `You are about to remove ${deleteTargetDetail.name}.`
+                    : "You are about to remove this skill."}
+                </p>
+                {deleteTargetDetail?.usedByAgents?.length ? (
+                  <div className="rounded-md border border-border px-3 py-3 text-muted-foreground">
+                    Currently used by {deleteTargetDetail.usedByAgents.map((agent) => agent.name).join(", ")}.
+                  </div>
+                ) : null}
+                {(deleteTargetDetail?.usedByAgents.length ?? 0) > 0 ? (
+                  <p className="text-muted-foreground">
+                    Detach this skill from all agents to enable removal.
+                  </p>
+                ) : null}
+              </>
+            )}
           </div>
           <DialogFooter>
-            {(deleteTargetDetail?.usedByAgents.length ?? 0) > 0 ? (
+            {(deleteTargetDetail?.usedByAgents.length ?? 0) > 0 && !deleteTargetSourceLocator ? (
               <Button variant="ghost" onClick={() => closeDeleteDialog(false)}>
                 Close
               </Button>
@@ -1115,10 +1261,10 @@ export function CompanySkills() {
                 </Button>
                 <Button
                   variant="destructive"
-                  onClick={() => deleteSkill.mutate()}
+                  onClick={() => deleteSkill.mutate(deleteTargetSourceLocator ?? undefined)}
-                  disabled={deleteSkill.isPending || !deleteTargetSkillId}
+                  disabled={deleteSkill.isPending || (!deleteTargetSkillId && !deleteTargetSourceLocator)}
                 >
-                  {deleteSkill.isPending ? "Removing..." : "Remove skill"}
+                  {deleteSkill.isPending ? "Removing..." : deleteTargetSourceLocator ? "Remove all from source" : "Remove skill"}
                 </Button>
               </>
             )}
@@ -1220,6 +1366,18 @@ export function CompanySkills() {
                 {importSkill.isPending ? <RefreshCw className="h-4 w-4 animate-spin" /> : "Add"}
               </Button>
             </div>
+            {source.trim().length > 0 && /github\.com|^[a-zA-Z0-9_-]+\/[a-zA-Z0-9_.-]+/.test(source.trim()) && (
+              <div className="mt-1 flex items-center gap-2 border-b border-border pb-2">
+                <input
+                  type="password"
+                  value={importAuthToken}
+                  onChange={(event) => setImportAuthToken(event.target.value)}
+                  placeholder="GitHub PAT (optional, for private repos)"
+                  className="w-full bg-transparent text-sm outline-none placeholder:text-muted-foreground"
+                  autoComplete="off"
+                />
+              </div>
+            )}
             {scanStatusMessage && (
               <p className="mt-3 text-xs text-muted-foreground">
                 {scanStatusMessage}
@@ -1284,7 +1442,7 @@ export function CompanySkills() {
             checkUpdatesPending={updateStatusQuery.isFetching}
             onInstallUpdate={() => installUpdate.mutate()}
             installUpdatePending={installUpdate.isPending}
-            onDelete={openDeleteDialog}
+            onDelete={handleDeleteSkill}
             deletePending={deleteSkill.isPending}
             onSave={() => saveFile.mutate()}
             savePending={saveFile.isPending}