fix(session): make worker branch namespace child-safe

backend/internal/cli/root_test.go

@@ -230,6 +230,7 @@ func TestStopDoesNotShutdownUnverifiedReusedPID(t *testing.T) {
 func TestStopUsesShutdownEndpoint(t *testing.T) {
 	cfg := setConfigEnv(t)
 	shutdownCalled := make(chan struct{}, 1)
+	var shutdownSeen atomic.Bool
 	srv := httptest.NewServer(http.HandlerFunc(func(w http.ResponseWriter, r *http.Request) {
 		switch r.URL.Path {
 		case "/healthz":
@@ -240,6 +241,7 @@ func TestStopUsesShutdownEndpoint(t *testing.T) {
 			if err := runfile.Remove(cfg.runFile); err != nil {
 				t.Fatal(err)
 			}
+			shutdownSeen.Store(true)
 			shutdownCalled <- struct{}{}
 			_, _ = fmt.Fprintf(w, `{"status":"shutting_down","service":%q,"pid":%d}`, daemonmeta.ServiceName, os.Getpid())
 		default:
@@ -253,7 +255,12 @@ func TestStopUsesShutdownEndpoint(t *testing.T) {
 	}
 
 	out, _, err := executeCLI(t, Deps{
-		ProcessAlive: func(pid int) bool { return pid == os.Getpid() },
+		ProcessAlive: func(pid int) bool {
+			if pid != os.Getpid() {
+				return false
+			}
+			return !shutdownSeen.Load()
+		},
 	}, "stop", "--json")
 	if err != nil {
 		t.Fatal(err)

backend/internal/cli/spawn.go

@@ -121,7 +121,7 @@ func newSpawnCommand(ctx *commandContext) *cobra.Command {
 	})
 	f.StringVar(&opts.project, "project", "", "Project id to spawn the session in (required)")
 	f.StringVar(&opts.harness, "harness", "", "Agent harness / --agent: claude-code, codex, aider, opencode, grok, droid, amp, agy, crush, cursor, qwen, copilot, goose, auggie, continue, devin, cline, kimi, kiro, kilocode, vibe, pi, autohand (default: the daemon's AO_AGENT)")
-	f.StringVar(&opts.branch, "branch", "", "Branch for the session worktree (default: ao/<session-id>)")
+	f.StringVar(&opts.branch, "branch", "", "Branch for the session worktree (default: ao/<session-id>/root)")
 	f.StringVar(&opts.prompt, "prompt", "", "Initial prompt for the agent")
 	f.StringVar(&opts.issue, "issue", "", "Issue id to associate with the session")
 	f.StringVar(&opts.claimPR, "claim-pr", "", "Immediately claim an existing PR for the spawned session")

backend/internal/cli/stop.go

@@ -112,21 +112,28 @@ func (c *commandContext) waitForStopped(ctx context.Context, pid int, runFilePat
 			return daemonStatus{}, err
 		}
 		alive := c.deps.ProcessAlive(pid)
-		if info == nil {
-			return daemonStatus{State: stateStopped, RunFile: runFilePath, DataDir: dataDir}, nil
-		}
 		if !alive {
 			// Only remove the run-file if it still belongs to the process we
 			// stopped. A concurrent `ao start` may have already written a new
 			// run-file for a different daemon; removing that would corrupt its
 			// handshake and make a live daemon look stopped.
-			if info.PID == pid {
+			if info != nil && info.PID == pid {
 				if err := runfile.Remove(runFilePath); err != nil {
 					return daemonStatus{}, err
 				}
 			}
 			return daemonStatus{State: stateStopped, RunFile: runFilePath, DataDir: dataDir}, nil
 		}
+		if info == nil {
+			// The daemon removes running.json before the process necessarily exits.
+			// Keep waiting so Windows releases inherited handles such as daemon.log
+			// before tests or callers clean up the data directory.
+			if !c.deps.Now().Before(deadline) {
+				return daemonStatus{}, fmt.Errorf("daemon pid %d removed run-file but did not exit within %s", pid, timeout)
+			}
+			c.deps.Sleep(100 * time.Millisecond)
+			continue
+		}
 		if !c.deps.Now().Before(deadline) {
 			return daemonStatus{}, fmt.Errorf("daemon pid %d did not stop within %s", pid, timeout)
 		}

backend/internal/cli/stop_test.go

@@ -81,3 +81,40 @@ func TestWaitForStoppedRemovesOwnRunFile(t *testing.T) {
 		t.Fatalf("own run-file should have been removed, got %#v", info)
 	}
 }
+
+func TestWaitForStoppedWaitsAfterRunFileRemovedUntilProcessExits(t *testing.T) {
+	dir := t.TempDir()
+	runFile := filepath.Join(dir, "running.json")
+
+	const stoppedPID = 1111
+	now := time.Unix(200, 0).UTC()
+	aliveChecks := 0
+	sleeps := 0
+	c := &commandContext{deps: Deps{
+		ProcessAlive: func(int) bool {
+			aliveChecks++
+			return aliveChecks < 3
+		},
+		Now: func() time.Time {
+			return now
+		},
+		Sleep: func(d time.Duration) {
+			sleeps++
+			now = now.Add(d)
+		},
+	}.withDefaults()}
+
+	st, err := c.waitForStopped(context.Background(), stoppedPID, runFile, dir, time.Second)
+	if err != nil {
+		t.Fatal(err)
+	}
+	if st.State != stateStopped {
+		t.Fatalf("state = %q, want stopped", st.State)
+	}
+	if sleeps == 0 {
+		t.Fatal("waitForStopped returned before waiting for process exit")
+	}
+	if aliveChecks < 3 {
+		t.Fatalf("process checks = %d, want at least 3", aliveChecks)
+	}
+}

backend/internal/observe/scm/observer.go

@@ -605,27 +605,40 @@ func (o *Observer) discoverNewPRs(ctx context.Context, sessionRepos []sessionRep
 }
 
 // matchSession picks the session that owns sourceBranch. A session owns the
-// branch when it is an exact match or a stacked descendant ("branch/..."). When
-// several session branches are prefixes of the same source branch the longest
-// (most specific) one wins, so a child session claims its own stacked PRs rather
-// than the ancestor session.
+// branch when it is an exact match or a stacked descendant ("branch/..."). The
+// default worker branch is a leaf named "<namespace>/root"; for that shape the
+// session also owns sibling branches under "<namespace>/..." so Git can create
+// child PR branches without colliding with the root ref. When several session
+// branches are prefixes of the same source branch the longest (most specific)
+// one wins, so a child session claims its own stacked PRs rather than the
+// ancestor session.
 func matchSession(candidates []sessionRepo, sourceBranch string) (sessionRepo, bool) {
 	var best sessionRepo
 	bestLen := -1
 	for _, sr := range candidates {
 		if sr.branch == "" {
 			continue
 		}
-		if sr.branch == sourceBranch || strings.HasPrefix(sourceBranch, sr.branch+"/") {
-			if len(sr.branch) > bestLen {
-				best = sr
-				bestLen = len(sr.branch)
+		for _, prefix := range sessionBranchPrefixes(sr.branch) {
+			if prefix == sourceBranch || strings.HasPrefix(sourceBranch, prefix+"/") {
+				if len(prefix) > bestLen {
+					best = sr
+					bestLen = len(prefix)
+				}
 			}
 		}
 	}
 	return best, bestLen >= 0
 }
 
+func sessionBranchPrefixes(branch string) []string {
+	prefixes := []string{branch}
+	if namespace, ok := strings.CutSuffix(branch, "/root"); ok && namespace != "" {
+		prefixes = append(prefixes, namespace)
+	}
+	return prefixes
+}
+
 func (o *Observer) selectRefreshCandidates(ctx context.Context, subjects map[string]*subject, guards map[string]repoGuardState, markRepoFailed func(ports.SCMRepo)) refreshSelection {
 	selection := refreshSelection{
 		subjectsByPR:  map[string]*subject{},

backend/internal/observe/scm/observer_test.go

@@ -485,6 +485,38 @@ func TestPoll_DiscoversStackedChildByBranchPrefix(t *testing.T) {
 	}
 }
 
+func TestPoll_DiscoversSiblingUnderRootSessionNamespace(t *testing.T) {
+	store := testStoreWithSession()
+	store.sessions[0].Metadata.Branch = "ao/p-1/root"
+	prObs := testObs(1)
+	prObs.PR.SourceBranch = "ao/p-1/fix"
+	prObs.PR.TargetBranch = "main"
+	provider := &fakeProvider{
+		repoGuards: map[string]ports.SCMGuardResult{prKey(testRepo, 0): {ETag: "v2"}},
+		openPRs: map[string][]ports.SCMPRObservation{prKey(testRepo, 0): {
+			{URL: "https://github.com/o/r/pull/1", Number: 1, SourceBranch: "ao/p-1/fix", HeadRepo: "o/r", TargetBranch: "main", HeadSHA: "sha1"},
+		}},
+		observations: map[string]ports.SCMObservation{prKey(testRepo, 1): prObs},
+	}
+	lc := &fakeLifecycle{}
+	obs := newTestObserver(store, provider, lc, time.Unix(1, 0).UTC())
+	if err := obs.Poll(context.Background()); err != nil {
+		t.Fatal(err)
+	}
+	if len(store.writes) == 0 {
+		t.Fatal("expected discovered PR write")
+	}
+	if got := store.writes[0].pr.SourceBranch; got != "ao/p-1/fix" {
+		t.Fatalf("source branch = %q, want ao/p-1/fix", got)
+	}
+	if got := store.writes[0].pr.SessionID; got != "p-1" {
+		t.Fatalf("session id = %q, want p-1", got)
+	}
+	if len(lc.observed) != 1 {
+		t.Fatalf("lifecycle observations = %d, want 1", len(lc.observed))
+	}
+}
+
 // A PR whose head branch matches a session branch but lives in a fork (its head
 // repo differs from the project repo) must not be auto-attributed: its commits
 // are not the session's work. It is neither fetched nor persisted.

backend/internal/session_manager/manager.go

@@ -616,9 +616,10 @@ func defaultSessionBranch(id domain.SessionID, kind domain.SessionKind, prefix s
 		return "ao/" + prefix + "-orchestrator"
 	}
 	// A fresh, unique branch per worker session: gitworktree can't add a worktree
-	// on a branch already checked out elsewhere (e.g. main), so default to one
-	// derived from the assigned session id.
-	return "ao/" + string(id)
+	// on a branch already checked out elsewhere (e.g. main). Put the root work
+	// branch under a session namespace so sibling PR branches such as
+	// ao/<session>/<topic> remain valid Git refs.
+	return "ao/" + string(id) + "/root"
 }
 
 func buildPrompt(cfg ports.SpawnConfig) string {
@@ -699,16 +700,17 @@ Only ping the orchestrator for true blockers, cross-session coordination, or dec
 
 // workerMultiPRPrompt explains the branch convention AO uses to attribute pull
 // requests to this session. A worker may open several PRs in one session: AO
-// tracks every open PR whose source branch is the session's own branch or a
-// descendant of it. Stacking a PR on top of another therefore only requires
-// branching off with a `<session-branch>/<topic>` name; PRs on unrelated
-// branches are attributed to whichever session owns their branch prefix.
+// tracks every open PR whose source branch is the session's own branch or lives
+// in the same session namespace. Stacking a PR on top of another therefore only
+// requires branching off with a `<session-namespace>/<topic>` name; PRs on
+// unrelated branches are attributed to whichever session owns their namespace.
 func workerMultiPRPrompt() string {
 	return `## Pull requests for this session
 
-You can open more than one pull request from this session. AO attributes a PR to you when its source branch is your session's working branch or a branch descended from it (a "/"-separated child like ` + "`your-branch/topic`" + `).
+You can open more than one pull request from this session. AO attributes a PR to you when its source branch is your session's working branch or another branch in the same session namespace.
 
-- For independent PRs, create each source branch as a child of your session branch (` + "`your-branch/<topic>`" + `) so it stays in this session's namespace, then open the PR targeting your base branch as usual. The PR can target the base branch; only the source branch needs to stay under your session branch for AO to track it.
+- If your current branch ends in ` + "`/root`" + `, create independent PR branches as siblings under the same namespace, for example ` + "`<namespace>/<topic>`" + ` from ` + "`<namespace>/root`" + `. Do not create ` + "`<namespace>/root/<topic>`" + `.
+- Otherwise, create each source branch as a child of your session branch (` + "`your-branch/<topic>`" + `) so it stays in this session's namespace, then open the PR targeting your base branch as usual. The PR can target the base branch; only the source branch needs to stay under your session namespace for AO to track it.
 - To stack a PR on top of another (so it merges after its parent), create the child branch from the parent branch and name it ` + "`<parent-branch>/<topic>`" + `, then target the parent branch in the PR. AO recognizes the stack from the branch relationship and will only nudge you to resolve conflicts on the bottom-most PR.
 
 Keep branch names within your session's branch namespace so AO can track every PR you open.`

backend/internal/session_manager/manager_test.go

@@ -550,9 +550,10 @@ func TestSpawn_DefaultsBranchFromSessionID(t *testing.T) {
 	if err != nil {
 		t.Fatal(err)
 	}
-	// An empty SpawnConfig.Branch defaults to a unique per-session branch.
-	if got := st.sessions[s.ID].Metadata.Branch; got != "ao/mer-1" {
-		t.Fatalf("default branch = %q, want ao/mer-1", got)
+	// An empty SpawnConfig.Branch defaults to a unique per-session root branch
+	// under a namespace that can also hold sibling PR branches.
+	if got := st.sessions[s.ID].Metadata.Branch; got != "ao/mer-1/root" {
+		t.Fatalf("default branch = %q, want ao/mer-1/root", got)
 	}
 }