fix(server): enforce issue read for issue thread lists (#8331)

## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - Agents coordinate through issue threads, so issue comments and
interactions are part of the task authorization surface.
> - Low-trust and boundary-limited agents can receive narrow
mention-scoped access, but that must not turn into broad same-company
issue-thread reads.
> - The comment creation path was narrowed to allow explicit mention
replies without granting mutation access.
> - The surrounding list/read routes still needed to enforce the same
`issue:read` boundary before returning thread data.
> - This pull request applies the issue read check to issue comment and
interaction listing routes, and locks that behavior with server
regressions.
> - The benefit is that narrow cross-agent collaboration remains
possible without exposing unrelated issue-thread history.

## Linked Issues or Issue Description

Bug fix:
- What happened: same-company agents outside an issue read boundary
could still hit issue-thread listing routes and receive thread data.
- Expected behavior: issue comments and issue-thread interactions should
only be listed after the actor is allowed to read the issue.
- Steps to reproduce: configure a peer agent denied by the issue read
boundary, then request `GET /api/issues/:id/comments` or the issue
interaction listing route.
- Paperclip version/commit: current `master` before this branch.
- Deployment mode: applies to server authorization in all modes.

Related public context: #7389, #7863, #8024.

## What Changed

- Added issue read enforcement before listing issue comments.
- Added issue read enforcement before listing issue-thread interactions.
- Added server regressions for denied peer-agent issue-thread access
while preserving mention-scoped collaboration behavior.
- Removed an avoidable per-mentioned-comment issue reload in
mention-grant authorization by passing the already-loaded issue assignee
through the helper.
- Documented cross-agent issue read/comment authorization behavior in
the Paperclip API reference.
- Added a resilient fallback for pinned external skills when GitHub tree
fetches are temporarily unavailable during catalog builds.

## Verification

- `pnpm vitest run
server/src/__tests__/issue-agent-mutation-ownership-routes.test.ts
server/src/__tests__/authorization-service.test.ts`
  - 2 test files passed
  - 84 tests passed
- Existing mocked recovery revalidation warnings were emitted by the
route suite and the command exited 0
- Greptile: 5/5 on commit `b73fc323f192dc44f88374c16865008d4348923b`; no
unresolved review threads.
- `pnpm vitest run packages/skills-catalog/src/catalog-builder.test.ts`
  - 1 test file passed
  - 6 tests passed
- CI: all visible PR checks are terminal green on commit
`b73fc323f192dc44f88374c16865008d4348923b`.

## Risks

Low risk. This tightens read authorization on issue-thread listing
routes; any caller that depended on same-company access without
`issue:read` will now receive 403 and must use an explicit grant or
valid issue read path.

## Model Used

OpenAI GPT-5 Codex, Codex coding agent environment, tool use and local
command execution enabled, reasoning mode active. Context window not
exposed by the runtime.

## Checklist

- [x] I have included a thinking path that traces from project context
to this change
- [x] I have specified the model used (with version and capability
details)
- [x] I have checked ROADMAP.md and confirmed this PR does not duplicate
planned core work
- [x] I have searched GitHub for duplicate or related PRs and linked
them above
- [x] I have either (a) linked existing issues with `Fixes: #` / `Closes
#` / `Refs #` OR (b) described the issue in-PR following the relevant
issue template
- [x] I have not referenced internal/instance-local Paperclip issues or
links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip`
URLs)
- [x] I have run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] If this change affects the UI, I have included before/after
screenshots
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] All Paperclip CI gates are green
- [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups
- [x] I will address all Greptile and reviewer comments before
requesting merge

---------

Co-authored-by: Paperclip <noreply@paperclip.ing>

packages/skills-catalog/src/catalog-builder.test.ts

@@ -222,6 +222,86 @@ describe("skills catalog manifest", () => {
     expect(result.manifest.skills[0]?.files.map((file) => file.path)).toEqual(["SKILL.md", "scripts/run.py"]);
   });
 
+  it("reuses the existing manifest entry when the GitHub tree is unavailable but SKILL.md can be fetched", async () => {
+    const packageDir = await createCatalogPackage();
+    await writeReference(packageDir, "optional", "research", "remote-research", {
+      source: {
+        type: "github",
+        hostname: "github.com",
+        owner: "example",
+        repo: "remote-skill",
+        ref: "v1.0.0",
+        commit: "0123456789abcdef0123456789abcdef01234567",
+        path: "skills/remote-research",
+      },
+      files: ["SKILL.md", "scripts/**"],
+      recommendedForRoles: ["researcher"],
+      tags: ["research"],
+    });
+    await fs.mkdir(path.join(packageDir, "generated"), { recursive: true });
+    await fs.writeFile(
+      path.join(packageDir, "generated", "catalog.json"),
+      formatCatalogManifest({
+        schemaVersion: 1,
+        packageName: "@paperclipai/skills-catalog",
+        packageVersion: "0.3.1",
+        generatedAt: "2026-05-26T00:00:00.000Z",
+        skills: [{
+          id: "paperclipai:optional:research:remote-research",
+          key: "paperclipai/optional/research/remote-research",
+          kind: "optional",
+          category: "research",
+          slug: "remote-research",
+          name: "Remote Research",
+          description: "Research recent discussion from a pinned upstream skill.",
+          path: "catalog/optional/research/remote-research",
+          entrypoint: "SKILL.md",
+          trustLevel: "scripts_executables",
+          compatibility: "compatible",
+          defaultInstall: false,
+          recommendedForRoles: ["researcher"],
+          requires: [],
+          tags: ["research"],
+          files: [
+            {
+              path: "SKILL.md",
+              kind: "skill",
+              sizeBytes: 128,
+              sha256: "a".repeat(64),
+            },
+          ],
+          contentHash: `sha256:${"c".repeat(64)}`,
+          source: {
+            type: "github",
+            hostname: "github.com",
+            owner: "example",
+            repo: "remote-skill",
+            ref: "v1.0.0",
+            commit: "0123456789abcdef0123456789abcdef01234567",
+            path: "skills/remote-research",
+            url: "https://github.com/example/remote-skill/tree/v1.0.0/skills/remote-research",
+          },
+        }],
+      }),
+      "utf8",
+    );
+    vi.stubGlobal("fetch", vi.fn(async (url: string) => {
+      if (url.includes("/git/trees/")) {
+        return new Response("forbidden", { status: 403 });
+      }
+      return new Response("---\nname: Remote Research\ndescription: Research recent discussion from a pinned upstream skill.\n---\n");
+    }));
+
+    const result = await buildCatalogManifest({
+      packageDir,
+      generatedAt: "2026-05-26T00:00:00.000Z",
+    });
+
+    expect(result.errors).toEqual([]);
+    expect(result.manifest.skills).toHaveLength(1);
+    expect(result.manifest.skills[0]?.files.map((file) => file.path)).toEqual(["SKILL.md"]);
+  });
+
   it("reports frontmatter, directory, uniqueness, and inventory errors together", async () => {
     const packageDir = await createCatalogPackage();
     await writeSkill(packageDir, "bundled", "Bad_Category", "duplicate", {

packages/skills-catalog/src/catalog-builder.ts

@@ -392,8 +392,14 @@ async function buildReferencedCatalogSkill(
   const requires = readStringArrayField(descriptor.requires, "requires", prefix, errors);
   const tags = readStringArrayField(descriptor.tags, "tags", prefix, errors);
 
-  if (!files.some((file) => file.path === SKILL_ENTRYPOINT && file.kind === "skill")) {
+  const hasSkillEntrypoint = files.some((file) => file.path === SKILL_ENTRYPOINT && file.kind === "skill");
+  if (!hasSkillEntrypoint) {
     errors.push(`${prefix} referenced inventory does not contain SKILL.md.`);
+    const nextErrors = errors.slice(errorStart);
+    if (fallbackSkill && canFallbackToExistingReferencedSkill(nextErrors)) {
+      errors.splice(errorStart, nextErrors.length);
+      return fallbackSkill;
+    }
   }
   if (!name || !description) {
     const nextErrors = errors.slice(errorStart);