fix(FN-3433): restore workspace llama-cpp docs index integrity

- Restore workspace llama-cpp extension path resolution in CLI command handling
- Add missing docs/README.md index entries and keep README/doc links aligned
- Add regression coverage for docs README index completeness and docker docs references
- Carry forward related workspace stability updates and test hardening from the branch

Fusion-Task-Id: FN-3433

packages/cli/src/__tests__/docs-readme-index.test.ts

@@ -0,0 +1,26 @@
+import { describe, expect, it } from "vitest";
+import { existsSync, readFileSync } from "node:fs";
+import { resolve } from "node:path";
+
+const workspaceRoot = resolve(import.meta.dirname, "../../../..");
+const docsReadmePath = resolve(workspaceRoot, "docs", "README.md");
+
+const requiredDocs = [
+  "docs/beads-dolt-sync-evaluation.md",
+  "docs/dev-server-modules.md",
+  "docs/research/pi-autoresearch-analysis.md",
+  "docs/research/research-hardening-preflight.md",
+] as const;
+
+describe("docs README index", () => {
+  it("includes links for required docs and those files exist", () => {
+    expect(existsSync(docsReadmePath)).toBe(true);
+    const docsReadme = readFileSync(docsReadmePath, "utf8");
+
+    for (const relativePath of requiredDocs) {
+      const readmeLinkPath = `./${relativePath.replace(/^docs\//, "")}`;
+      expect(docsReadme).toContain(`(${readmeLinkPath})`);
+      expect(existsSync(resolve(workspaceRoot, relativePath))).toBe(true);
+    }
+  });
+});