fix(server): storage cleanup no longer counts pnpm clones as freed space

apps/server/src/storageCleanup.test.ts

@@ -1241,6 +1241,59 @@ describe("storage cleanup reports and local file policies", () => {
       }),
     ),
   );
+  it.live.each(["same-device", "other-device", "no-manifest"] as const)(
+    "counts the pnpm virtual store only when its store forces copies (%s)",
+    (store) =>
+      runCleanupTest(
+        Effect.gen(function* () {
+          const fs = yield* FileSystem.FileSystem;
+          const storeDir = yield* fs.makeTempDirectoryScoped({ prefix: "pnpm-store-" });
+          const { service, worktree, setPolicy } = yield* cleanupFixture().pipe(
+            Effect.provideService(FileSystem.FileSystem, {
+              ...fs,
+              stat: (target) =>
+                fs
+                  .stat(target)
+                  .pipe(
+                    Effect.map((info) =>
+                      store === "other-device" && target === storeDir
+                        ? { ...info, dev: info.dev + 1n }
+                        : info,
+                    ),
+                  ),
+            }),
+          );
+          setPolicy("tracked-changes");
+          const nodeModules = `${worktree}/node_modules`;
+          yield* fs.makeDirectory(`${nodeModules}/.pnpm/pkg@1.0.0`, { recursive: true });
+          yield* fs.makeDirectory(`${nodeModules}/.vite`);
+          yield* fs.writeFileString(
+            `${nodeModules}/.pnpm/pkg@1.0.0/index.js`,
+            "clone ".repeat(10_000),
+          );
+          yield* fs.writeFileString(`${nodeModules}/.vite/deps.js`, "cache");
+          if (store !== "no-manifest")
+            yield* fs.writeFileString(
+              `${nodeModules}/.modules.yaml`,
+              JSON.stringify({ storeDir, virtualStoreDir: ".pnpm" }),
+            );
+          const counted = [
+            ...(yield* fs.readDirectory(worktree)).flatMap((name) =>
+              name === "node_modules" ? [] : [`${worktree}/${name}`],
+            ),
+            `${nodeModules}/.vite/deps.js`,
+            ...(store === "no-manifest" ? [] : [`${nodeModules}/.modules.yaml`]),
+            ...(store === "same-device" ? [] : [`${nodeModules}/.pnpm/pkg@1.0.0/index.js`]),
+          ];
+          const bytes = (yield* Effect.forEach(counted, (file) => allocatedBytes(fs, file))).reduce(
+            (sum, size) => sum + size,
+            0,
+          );
+          const report = yield* service.runNow;
+          expect(report.entries[0]).toMatchObject({ outcome: "removed", bytes });
+        }),
+      ),
+  );
   it.live("still removes a worktree when measuring its size fails", () =>
     runCleanupTest(
       Effect.gen(function* () {

apps/server/src/storageCleanup.ts

@@ -32,6 +32,7 @@ import type { PlatformError } from "effect/PlatformError";
 import * as Schedule from "effect/Schedule";
 import * as Stream from "effect/Stream";
 import * as SubscriptionRef from "effect/SubscriptionRef";
+import { parse as parseYaml } from "yaml";
 
 import * as ServerConfig from "./config.ts";
 import * as GitManager from "./git/GitManager.ts";
@@ -55,6 +56,13 @@ const decodeCleanupThread = Schema.decodeUnknownEffect(
 const decodeCleanupSession = Schema.decodeUnknownEffect(
   Schema.fromJsonString(OrchestrationV2ProviderSessionJson),
 );
+// pnpm 11 writes this file as JSON, older versions as YAML.
+const decodePnpmModulesManifest = Schema.decodeUnknownEffect(
+  Schema.Struct({
+    storeDir: Schema.String,
+    virtualStoreDir: Schema.optional(Schema.String),
+  }),
+);
 
 const DAY_MS = 86_400_000;
 // After a settle, the project's settle script needs time to open its
@@ -247,14 +255,35 @@ const make = Effect.gen(function* () {
         );
       });
 
+  // pnpm imports packages by clone or reflink when its store shares a device
+  // with the worktree. Those files have one link but share blocks with the
+  // store, so removing them frees almost nothing. A store on another device
+  // forces real copies, which still count.
+  const sharedPnpmVirtualStore = Effect.fnUntraced(
+    function* (root: string) {
+      const nodeModules = path.join(root, "node_modules");
+      const text = yield* fs.readFileString(path.join(nodeModules, ".modules.yaml"));
+      const manifest = yield* decodePnpmModulesManifest(yield* Effect.try(() => parseYaml(text)));
+      const virtualStore = path.resolve(nodeModules, manifest.virtualStoreDir ?? ".pnpm");
+      const [store, virtual] = yield* Effect.all([
+        fs.stat(manifest.storeDir),
+        fs.stat(virtualStore),
+      ]);
+      return store.dev === virtual.dev ? virtualStore : null;
+    },
+    Effect.orElseSucceed(() => null),
+  );
+
   const measureWorktree = Effect.fn("storageCleanup.measureWorktree")(
     function* (worktreePath: string) {
       const root = yield* fs.realPath(worktreePath);
+      const skipped = yield* sharedPnpmVirtualStore(root);
       const pending = [root];
       let entries = 1;
       let bytes = 0;
       while (pending.length > 0) {
         const target = pending.pop()!;
+        if (target === skipped) continue;
         // Effect's stat follows links. Probe with readLink first to get lstat
         // semantics, including skipping dangling links and directory links.
         const isLink = yield* fs.readLink(target).pipe(