Consolidate Reader source ownership and pinned application instances

Add exact recursive source checkout, independent Git/jj developer workbenches and source-only backup/recovery commands, with Workspace instance binding outside source. Qualify two empty Reader Graphs, packaged source commands, Agent VM compilation, exact Gitea read grants and reconciled Reader settings/annotation stability. Publish checked Reader Package/root revisions to canonical review branches and retention tags, retain all 57 repositories independently in private versioned storage, verify downloaded-backup recovery and advance the example pin.

Add bounded Central pin acquisition and selection-specific read-only identities, qualified against all 57 canonical repositories without write authority. Replace regex fork dependency discovery with compiler-parsed lock imports and rewrite proposals; preserve source identities and unrelated files, passing instance binding through packed and ordinary host checks.

Hosted run-pin versus authoring preparation and maintained duplicate removal remain pending. Live source selections, Template defaults and default source branches are unchanged.

src/capability-language/source-backup.ts

@@ -0,0 +1,117 @@
+import { execFile as callback } from "node:child_process";
+import { promisify } from "node:util";
+import { createHash } from "node:crypto";
+import { createReadStream } from "node:fs";
+import { lstat, mkdir, mkdtemp, readFile, rename, rm, writeFile } from "node:fs/promises";
+import path from "node:path";
+import { pathToFileURL } from "node:url";
+import { retentionTagForCommit } from "../resource-lock/index.js";
+import { materializeWorkspaceSources, workspaceSourcePin, type WorkspaceSourcePin } from "./source-closure.js";
+
+const exec = promisify(callback);
+type SourceBackup = {
+  formatVersion: 1;
+  root: WorkspaceSourcePin;
+  repositories: Array<{ repository: string; commits: string[]; bundle: string; sha256: string }>;
+};
+async function hash(filename: string) {
+  const digest = createHash("sha256");
+  for await (const chunk of createReadStream(filename)) digest.update(chunk);
+  return digest.digest("hex");
+}
+
+/** Source-only backup: no Graph state, checkout instructions or credentials.
+ * Git bundles retain exact commits and their ancestors without needing a forge.
+ * Storage/retention of the resulting directory belongs to the operator. */
+export async function backupWorkspaceSources(options: {
+  source: WorkspaceSourcePin;
+  directory: string;
+  output: string;
+  locations?: Record<string, string>;
+}): Promise<SourceBackup> {
+  const output = path.resolve(options.output);
+  if (
+    await lstat(output).catch((error: NodeJS.ErrnoException) => {
+      if (error.code !== "ENOENT") throw error;
+      return null;
+    })
+  )
+    throw Error("Source backup destination must not exist");
+  const closure = await materializeWorkspaceSources(options);
+  const grouped = new Map<string, Map<string, string>>();
+  for (const entry of closure.resources) {
+    const commits = grouped.get(entry.repository) ?? new Map<string, string>();
+    commits.set(entry.commit, path.join(path.resolve(options.directory), entry.directory));
+    grouped.set(entry.repository, commits);
+  }
+  await mkdir(path.dirname(output), { recursive: true });
+  const staging = await mkdtemp(path.join(path.dirname(output), ".source-backup-"));
+  const manifest: SourceBackup = { formatVersion: 1, root: closure.root, repositories: [] };
+  try {
+    for (const [repository, commits] of [...grouped].sort(([a], [b]) => a.localeCompare(b))) {
+      const bundle = createHash("sha256").update(repository).digest("hex") + ".bundle";
+      const gitDirectory = await mkdtemp(path.join(staging, ".git-"));
+      try {
+        await exec("git", ["init", "--bare", gitDirectory]);
+        const refs: string[] = [];
+        for (const [commit, checkout] of commits) {
+          const ref = retentionTagForCommit(commit);
+          await exec("git", ["-C", gitDirectory, "fetch", "--no-tags", "--", checkout, `${ref}:${ref}`]);
+          refs.push(ref);
+        }
+        await exec("git", ["-C", gitDirectory, "bundle", "create", path.join(staging, bundle), ...refs]);
+      } finally {
+        await rm(gitDirectory, { recursive: true, force: true });
+      }
+      manifest.repositories.push({
+        repository,
+        commits: [...commits.keys()].sort(),
+        bundle,
+        sha256: await hash(path.join(staging, bundle)),
+      });
+    }
+    await writeFile(path.join(staging, "backup.json"), JSON.stringify(manifest, null, 2) + "\n", { mode: 0o600 });
+    await rename(staging, output);
+    return manifest;
+  } finally {
+    await rm(staging, { recursive: true, force: true });
+  }
+}
+
+export async function restoreWorkspaceSources(options: { backup: string; directory: string }) {
+  const backup = path.resolve(options.backup);
+  const filename = path.join(backup, "backup.json");
+  const info = await lstat(filename);
+  if (!info.isFile() || info.isSymbolicLink() || info.size > 1024 * 1024) throw Error("Invalid source backup manifest");
+  const manifest = JSON.parse(await readFile(filename, "utf8")) as SourceBackup;
+  if (
+    manifest.formatVersion !== 1 ||
+    !Array.isArray(manifest.repositories) ||
+    !manifest.repositories.length ||
+    manifest.repositories.length > 256
+  )
+    throw Error("Invalid source backup manifest");
+  const root = workspaceSourcePin(manifest.root);
+  const locations: Record<string, string> = {};
+  for (const entry of manifest.repositories) {
+    if (!entry || !Array.isArray(entry.commits) || !entry.commits.length || entry.commits.length > 256)
+      throw Error("Invalid source backup entry");
+    for (const commit of entry.commits) workspaceSourcePin({ repository: entry.repository, commit });
+    if (Object.hasOwn(locations, entry.repository)) throw Error("Duplicate source backup repository");
+    const expected = createHash("sha256").update(entry.repository).digest("hex") + ".bundle";
+    if (entry.bundle !== expected || !/^[a-f0-9]{64}$/.test(entry.sha256))
+      throw Error("Invalid source backup bundle identity");
+    const bundle = path.join(backup, expected);
+    const stat = await lstat(bundle);
+    if (!stat.isFile() || stat.isSymbolicLink() || (await hash(bundle)) !== entry.sha256)
+      throw Error("Source backup bundle integrity mismatch");
+    locations[entry.repository] = pathToFileURL(bundle).href;
+  }
+  if (
+    !manifest.repositories.some((entry) => entry.repository === root.repository && entry.commits.includes(root.commit))
+  )
+    throw Error("Source backup does not retain its root commit");
+  // Every discovered dependency must use the backup. Never fall through to the
+  // original forge if a manifest omits a required repository.
+  return materializeWorkspaceSources({ source: root, directory: options.directory, locations, requireLocations: true });
+}