fix: normalize planning doc paths and restore forkScoped for background upstream refresh

- Replace absolute developer-local paths (/Users/julius/.t3/worktrees/...)
  in .plans/effect-atom.md with repository-relative paths
- Restore Effect.forkScoped (instead of Effect.forkDetach) for the
  background refreshCheckedOutBranchUpstream call so the fiber is tied
  to the enclosing scope and properly interrupted during shutdown

Author: cursoragent

.plans/effect-atom.md

@@ -1,42 +1,42 @@
 # Replace React Query With AtomRpc + Atom State
 
 ## Summary
-- Use `effect/unstable/reactivity/AtomRpc` over the existing `WsRpcGroup`; stop wrapping RPC in promises via [wsRpcClient.ts](/Users/julius/.t3/worktrees/codething-mvp/effect-http-router/apps/web/src/wsRpcClient.ts) and [wsNativeApi.ts](/Users/julius/.t3/worktrees/codething-mvp/effect-http-router/apps/web/src/wsNativeApi.ts).
+- Use `effect/unstable/reactivity/AtomRpc` over the existing `WsRpcGroup`; stop wrapping RPC in promises via [wsRpcClient.ts](apps/web/src/wsRpcClient.ts) and [wsNativeApi.ts](apps/web/src/wsNativeApi.ts).
 - Keep Zustand for orchestration read model and UI state.
 - Keep a narrow `desktopBridge` adapter for dialogs, menus, external links, theme, and updater APIs.
 - Do not introduce Suspense in this migration. Atom-backed hooks should keep returning `data`, `error`, `isLoading|isPending`, `refresh`, and `mutateAsync`-style surfaces so component churn stays low.
 
 ## Target Architecture
-- Extract the websocket `RpcClient.Protocol` layer from [wsTransport.ts](/Users/julius/.t3/worktrees/codething-mvp/effect-http-router/apps/web/src/wsTransport.ts) into `rpc/protocol.ts`.
+- Extract the websocket `RpcClient.Protocol` layer from [wsTransport.ts](apps/web/src/wsTransport.ts) into `rpc/protocol.ts`.
 - Define one `AtomRpc.Service` for `WsRpcGroup` in `rpc/client.ts`.
 - Add `rpc/invalidation.ts` with explicit scoped invalidation keys: `git:${cwd}`, `project:${cwd}`, `checkpoint:${threadId}`, `server-config`.
 - Add `platform/desktopBridge.ts` as the only browser/desktop facade.
-- Remove from web by the end: [wsNativeApi.ts](/Users/julius/.t3/worktrees/codething-mvp/effect-http-router/apps/web/src/wsNativeApi.ts), [nativeApi.ts](/Users/julius/.t3/worktrees/codething-mvp/effect-http-router/apps/web/src/nativeApi.ts), [wsNativeApiState.ts](/Users/julius/.t3/worktrees/codething-mvp/effect-http-router/apps/web/src/wsNativeApiState.ts), [wsNativeApiAtoms.tsx](/Users/julius/.t3/worktrees/codething-mvp/effect-http-router/apps/web/src/wsNativeApiAtoms.tsx), [wsRpcClient.ts](/Users/julius/.t3/worktrees/codething-mvp/effect-http-router/apps/web/src/wsRpcClient.ts), and all `*ReactQuery.ts` modules.
+- Remove from web by the end: [wsNativeApi.ts](apps/web/src/wsNativeApi.ts), [nativeApi.ts](apps/web/src/nativeApi.ts), [wsNativeApiState.ts](apps/web/src/wsNativeApiState.ts), [wsNativeApiAtoms.tsx](apps/web/src/wsNativeApiAtoms.tsx), [wsRpcClient.ts](apps/web/src/wsRpcClient.ts), and all `*ReactQuery.ts` modules.
 
 ## Phase 1: Infrastructure First
-1. Extract the shared websocket RPC protocol layer from [wsTransport.ts](/Users/julius/.t3/worktrees/codething-mvp/effect-http-router/apps/web/src/wsTransport.ts) without changing behavior.
+1. Extract the shared websocket RPC protocol layer from [wsTransport.ts](apps/web/src/wsTransport.ts) without changing behavior.
 2. Build the AtomRpc client on top of that layer.
 3. Add one temporary `runRpc` helper for imperative handlers that still want `Promise` ergonomics; it must call the AtomRpc service directly and must not reintroduce a facade object.
 4. Replace manual registry wiring with one app-level registry provider based on `@effect/atom-react`.
 5. Land this as a no-behavior-change PR.
 
 ## Phase 2: Replace `wsNativeApi`-Owned Push State
 1. Migrate welcome/config/provider/settings state first, because it is already atom-shaped and is the lowest-risk way to delete `wsNativeApi` responsibilities.
-2. Replace [wsNativeApiState.ts](/Users/julius/.t3/worktrees/codething-mvp/effect-http-router/apps/web/src/wsNativeApiState.ts) with `rpc/serverState.ts`, updated directly from `subscribeServerLifecycle` and `subscribeServerConfig`.
+2. Replace [wsNativeApiState.ts](apps/web/src/wsNativeApiState.ts) with `rpc/serverState.ts`, updated directly from `subscribeServerLifecycle` and `subscribeServerConfig`.
 3. Keep the current hook names for one PR: `useServerConfig`, `useServerSettings`, `useServerProviders`, `useServerKeybindings`, `useServerWelcomeSubscription`, `useServerConfigUpdatedSubscription`.
-4. Move bootstrap side effects out of [wsNativeApiAtoms.tsx](/Users/julius/.t3/worktrees/codething-mvp/effect-http-router/apps/web/src/wsNativeApiAtoms.tsx) into a new root bootstrap component mounted from [__root.tsx](/Users/julius/.t3/worktrees/codething-mvp/effect-http-router/apps/web/src/routes/__root.tsx).
-5. Delete the `server.getConfig()` fallback logic from [wsNativeApi.ts](/Users/julius/.t3/worktrees/codething-mvp/effect-http-router/apps/web/src/wsNativeApi.ts); snapshot fetch now lives beside the stream atoms.
+4. Move bootstrap side effects out of [wsNativeApiAtoms.tsx](apps/web/src/wsNativeApiAtoms.tsx) into a new root bootstrap component mounted from [__root.tsx](apps/web/src/routes/__root.tsx).
+5. Delete the `server.getConfig()` fallback logic from [wsNativeApi.ts](apps/web/src/wsNativeApi.ts); snapshot fetch now lives beside the stream atoms.
 
 ## Phase 3: Replace React Query Domain By Domain
-1. Replace [gitReactQuery.ts](/Users/julius/.t3/worktrees/codething-mvp/effect-http-router/apps/web/src/lib/gitReactQuery.ts) first.
+1. Replace [gitReactQuery.ts](apps/web/src/lib/gitReactQuery.ts) first.
 2. Add `rpc/gitAtoms.ts` and `rpc/useGit.ts` with `useGitStatus`, `useGitBranches`, `useResolvePullRequest`, and `useGitMutation`.
 3. Mutation settlement must invalidate scoped keys, not a global cache. `checkout`, `pull`, `init`, `createWorktree`, `removeWorktree`, `preparePullRequestThread`, and stacked actions invalidate `git:${cwd}`. Worktree create/remove also invalidates `project:${cwd}`.
-4. Replace [projectReactQuery.ts](/Users/julius/.t3/worktrees/codething-mvp/effect-http-router/apps/web/src/lib/projectReactQuery.ts) second. `useProjectSearchEntries` must preserve current “keep previous results while loading” behavior.
-5. Replace [providerReactQuery.ts](/Users/julius/.t3/worktrees/codething-mvp/effect-http-router/apps/web/src/lib/providerReactQuery.ts) third. Preserve current checkpoint error normalization and retry/backoff semantics inside the atom effect. Invalidate by `checkpoint:${threadId}`.
+4. Replace [projectReactQuery.ts](apps/web/src/lib/projectReactQuery.ts) second. `useProjectSearchEntries` must preserve current “keep previous results while loading” behavior.
+5. Replace [providerReactQuery.ts](apps/web/src/lib/providerReactQuery.ts) third. Preserve current checkpoint error normalization and retry/backoff semantics inside the atom effect. Invalidate by `checkpoint:${threadId}`.
 6. Defer the desktop updater until the last phase.
 
 ## Phase 4: Move Root Invalidation Off `queryClient`
-1. In [__root.tsx](/Users/julius/.t3/worktrees/codething-mvp/effect-http-router/apps/web/src/routes/__root.tsx), remove `QueryClient` usage and replace the throttled `invalidateQueries` block with throttled invalidation helpers.
+1. In [__root.tsx](apps/web/src/routes/__root.tsx), remove `QueryClient` usage and replace the throttled `invalidateQueries` block with throttled invalidation helpers.
 2. Keep Zustand orchestration/event application unchanged.
 3. Map current effects exactly:
 - git or checkpoint-affecting orchestration events touch `checkpoint:${threadId}`
@@ -50,14 +50,14 @@
 - `rpc/gitActions.ts`
 - `rpc/projectActions.ts`
 - `platform/desktopBridge.ts`
-2. Migrate direct [nativeApi.ts](/Users/julius/.t3/worktrees/codething-mvp/effect-http-router/apps/web/src/nativeApi.ts) callers by domain, not file-by-file: git-heavy components first, then orchestration/thread actions, then shell/dialog helpers.
-3. After the last caller is gone, delete [nativeApi.ts](/Users/julius/.t3/worktrees/codething-mvp/effect-http-router/apps/web/src/nativeApi.ts) and the `window.nativeApi` fallback entirely.
-4. In the final cleanup PR, remove `NativeApi` from [ipc.ts](/Users/julius/.t3/worktrees/codething-mvp/effect-http-router/packages/contracts/src/ipc.ts) if nothing outside web still needs it.
+2. Migrate direct [nativeApi.ts](apps/web/src/nativeApi.ts) callers by domain, not file-by-file: git-heavy components first, then orchestration/thread actions, then shell/dialog helpers.
+3. After the last caller is gone, delete [nativeApi.ts](apps/web/src/nativeApi.ts) and the `window.nativeApi` fallback entirely.
+4. In the final cleanup PR, remove `NativeApi` from [ipc.ts](packages/contracts/src/ipc.ts) if nothing outside web still needs it.
 
 ## Phase 6: Remove React Query Completely
 1. Delete `@tanstack/react-query` from `apps/web/package.json`.
-2. Remove `QueryClientProvider` and router context from [router.ts](/Users/julius/.t3/worktrees/codething-mvp/effect-http-router/apps/web/src/router.ts) and [__root.tsx](/Users/julius/.t3/worktrees/codething-mvp/effect-http-router/apps/web/src/routes/__root.tsx).
-3. Replace [desktopUpdateReactQuery.ts](/Users/julius/.t3/worktrees/codething-mvp/effect-http-router/apps/web/src/lib/desktopUpdateReactQuery.ts) with a writable atom plus `desktopBridge.onUpdateState`.
+2. Remove `QueryClientProvider` and router context from [router.ts](apps/web/src/router.ts) and [__root.tsx](apps/web/src/routes/__root.tsx).
+3. Replace [desktopUpdateReactQuery.ts](apps/web/src/lib/desktopUpdateReactQuery.ts) with a writable atom plus `desktopBridge.onUpdateState`.
 4. Delete the old query-option tests.
 
 ## Public Interfaces And Types
@@ -70,8 +70,8 @@
 ## Test Plan
 - Add unit tests for `rpc/serverState.ts`: snapshot bootstrapping, stream replay, provider/settings updates.
 - Add unit tests for git/project/checkpoint hooks: loading, error mapping, retry behavior, invalidation, keep-previous-result behavior.
-- Update the browser harness in [wsRpcHarness.ts](/Users/julius/.t3/worktrees/codething-mvp/effect-http-router/apps/web/test/wsRpcHarness.ts) to assert direct RPC + atom behavior instead of `__resetNativeApiForTests`.
-- Replace [wsNativeApi.test.ts](/Users/julius/.t3/worktrees/codething-mvp/effect-http-router/apps/web/src/wsNativeApi.test.ts), `gitReactQuery.test.ts`, `providerReactQuery.test.ts`, and `desktopUpdateReactQuery.test.ts` with equivalent atom-backed coverage.
+- Update the browser harness in [wsRpcHarness.ts](apps/web/test/wsRpcHarness.ts) to assert direct RPC + atom behavior instead of `__resetNativeApiForTests`.
+- Replace [wsNativeApi.test.ts](apps/web/src/wsNativeApi.test.ts), `gitReactQuery.test.ts`, `providerReactQuery.test.ts`, and `desktopUpdateReactQuery.test.ts` with equivalent atom-backed coverage.
 - Acceptance scenarios:
 - welcome still bootstraps snapshot and navigation
 - keybindings toast still responds to config stream updates

apps/server/src/git/Layers/GitCore.ts

@@ -1943,7 +1943,7 @@ export const makeGitCore = Effect.fn("makeGitCore")(function* (options?: {
       // Refresh upstream refs in the background so checkout remains responsive.
       yield* refreshCheckedOutBranchUpstream(input.cwd).pipe(
         Effect.ignoreCause({ log: true }),
-        Effect.forkDetach({ startImmediately: true }),
+        Effect.forkScoped,
       );
     },
   );