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/development-sources.ts

@@ -0,0 +1,93 @@
+import { execFile as callback } from "node:child_process";
+import { promisify } from "node:util";
+import { randomUUID } from "node:crypto";
+import { mkdir, mkdtemp, lstat, rename, rm, writeFile } from "node:fs/promises";
+import path from "node:path";
+import { materializeWorkspaceSources, workspaceSourcePin, type WorkspaceSourcePin } from "./source-closure.js";
+
+const exec = promisify(callback);
+
+/** Developer workflow, not an ordinary Workspace Agent's implicit permission
+ * to publish against canonical repositories. Creates independent Git/jj copies,
+ * with instance binding outside committed source. No Graph is started here.
+ */
+export async function prepareDevelopmentSources(options: {
+  source: WorkspaceSourcePin;
+  directory: string;
+  cacheDirectory: string;
+  locations?: Record<string, string>;
+}) {
+  const source = workspaceSourcePin(options.source);
+  const destination = path.resolve(options.directory);
+  const cache = path.resolve(options.cacheDirectory);
+  if (cache === destination || cache.startsWith(destination + path.sep))
+    throw Error("The retained source cache must live outside the disposable workbench");
+  if (
+    await lstat(destination).catch((error: NodeJS.ErrnoException) => {
+      if (error.code !== "ENOENT") throw error;
+      return null;
+    })
+  )
+    throw Error("Choose a new development workbench directory; existing checkouts are never overwritten");
+  const closure = await materializeWorkspaceSources({
+    source,
+    directory: options.cacheDirectory,
+    locations: options.locations,
+  });
+  const origins = new Set<string>();
+  for (const entry of closure.resources) {
+    const identity = `${entry.kind}:${entry.repository}`;
+    if (origins.has(identity)) throw Error("Multiple revisions of one repository require explicit editable selection");
+    origins.add(identity);
+  }
+  const parent = path.dirname(destination);
+  await mkdir(parent, { recursive: true });
+  const staging = await mkdtemp(path.join(parent, ".development-sources-"));
+  const workspaceId = randomUUID();
+  try {
+    const resources = [];
+    for (const entry of closure.resources) {
+      const relative = entry.kind === "workspace" ? "root" : "resources/" + entry.directory;
+      const checkout = path.join(staging, relative);
+      await mkdir(path.dirname(checkout), { recursive: true });
+      await exec("git", [
+        "clone",
+        "--no-hardlinks",
+        "--",
+        path.join(path.resolve(options.cacheDirectory), entry.directory),
+        checkout,
+      ]);
+      await exec("git", ["remote", "set-url", "origin", entry.repository], { cwd: checkout });
+      await exec("git", ["checkout", "--detach", entry.commit], { cwd: checkout });
+      await exec("jj", ["git", "init", "--colocate"], {
+        cwd: checkout,
+        env: { ...process.env, QUIXOS_JJ_NO_CHECKPOINT: "1", QUIXOS_SUBTREE_PUBLISH: "0" },
+      });
+      await exec("jj", ["describe", "-m", "Develop canonical application source"], {
+        cwd: checkout,
+        env: { ...process.env, QUIXOS_JJ_NO_CHECKPOINT: "1", QUIXOS_SUBTREE_PUBLISH: "0" },
+      });
+      if (entry.kind !== "workspace")
+        resources.push({
+          kind: entry.kind,
+          directory: relative,
+          source: { resolver: "git", repository: entry.repository, commit: entry.commit },
+        });
+    }
+    await mkdir(path.join(staging, ".quixos"), { mode: 0o700 });
+    await writeFile(
+      path.join(staging, ".quixos/resource-graph.json"),
+      JSON.stringify({ formatVersion: 1, workspaceId, resources }, null, 2) + "\n",
+      { mode: 0o600 },
+    );
+    await writeFile(
+      path.join(staging, ".quixos/development-source.json"),
+      JSON.stringify({ source, workspaceId }, null, 2) + "\n",
+      { mode: 0o600 },
+    );
+    await rename(staging, destination);
+    return { directory: destination, source, workspaceId, repositories: closure.resources.length };
+  } finally {
+    await rm(staging, { recursive: true, force: true });
+  }
+}