fix(cli): harden daemon control surface and stop CLI from writing the store

Addresses review findings on PR #53 (on top of the rebase onto main).

- doctor: stop opening/migrating SQLite. The daemon is the sole store
  writer/migrator (architecture.md §7); the CLI must not run migrations or
  open a second writer against a DB a live daemon owns. doctor now reports
  database-file presence and gains --json.
- stop: only remove running.json when it still belongs to the PID we
  stopped, so a concurrent `ao start` that wrote a new run-file is not
  clobbered into looking stopped.
- httpd: gate POST /shutdown to loopback callers with no Origin header,
  closing the CSRF / DNS-rebinding vector against an unauthenticated,
  state-changing endpoint.
- start: detach the spawned daemon into its own session/process group so a
  Ctrl-C while `ao start` waits for readiness doesn't also kill it.
- cli: exit 2 for usage errors (bad flag / arg count) vs 1 for runtime
  failures.
- daemon: unexport newLogger (only used in-package).
- tests: /shutdown guard (cross-origin + rebinding) and stop run-file
  ownership guard.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

backend/cmd/ao/main.go

@@ -10,6 +10,6 @@ import (
 func main() {
 	if err := cli.Execute(); err != nil {
 		fmt.Fprintln(os.Stderr, err)
-		os.Exit(1)
+		os.Exit(cli.ExitCode(err))
 	}
 }

backend/internal/cli/completion.go

@@ -8,9 +8,14 @@ import (
 
 func newCompletionCommand() *cobra.Command {
 	return &cobra.Command{
-		Use:       "completion [bash|zsh|fish|powershell]",
-		Short:     "Generate shell completion scripts",
-		Args:      cobra.ExactArgs(1),
+		Use:   "completion [bash|zsh|fish|powershell]",
+		Short: "Generate shell completion scripts",
+		Args: func(cmd *cobra.Command, args []string) error {
+			if err := cobra.ExactArgs(1)(cmd, args); err != nil {
+				return usageError{err}
+			}
+			return nil
+		},
 		ValidArgs: []string{"bash", "zsh", "fish", "powershell"},
 		RunE: func(cmd *cobra.Command, args []string) error {
 			root := cmd.Root()

backend/internal/cli/doctor.go

@@ -2,13 +2,15 @@ package cli
 
 import (
 	"context"
+	"errors"
 	"fmt"
+	"io/fs"
 	"os"
+	"path/filepath"
 
 	"github.com/spf13/cobra"
 
 	"github.com/aoagents/agent-orchestrator/backend/internal/config"
-	"github.com/aoagents/agent-orchestrator/backend/internal/storage/sqlite"
 )
 
 type doctorLevel string
@@ -20,34 +22,53 @@ const (
 )
 
 type doctorCheck struct {
-	Level   doctorLevel
-	Name    string
-	Message string
+	Level   doctorLevel `json:"level"`
+	Name    string      `json:"name"`
+	Message string      `json:"message"`
+}
+
+type doctorReport struct {
+	OK       bool          `json:"ok"`
+	Failures int           `json:"failures"`
+	Checks   []doctorCheck `json:"checks"`
 }
 
 func newDoctorCommand(ctx *commandContext) *cobra.Command {
-	return &cobra.Command{
+	var asJSON bool
+	cmd := &cobra.Command{
 		Use:   "doctor",
 		Short: "Run local AO health checks",
 		RunE: func(cmd *cobra.Command, args []string) error {
 			checks := ctx.runDoctor(cmd.Context())
-			for _, check := range checks {
-				if _, err := fmt.Fprintf(cmd.OutOrStdout(), "%s %s: %s\n", check.Level, check.Name, check.Message); err != nil {
-					return err
-				}
-			}
-			var failures int
+			failures := 0
 			for _, check := range checks {
 				if check.Level == doctorFail {
 					failures++
 				}
 			}
+
+			if asJSON {
+				if err := writeJSON(cmd.OutOrStdout(), doctorReport{
+					OK: failures == 0, Failures: failures, Checks: checks,
+				}); err != nil {
+					return err
+				}
+			} else {
+				for _, check := range checks {
+					if _, err := fmt.Fprintf(cmd.OutOrStdout(), "%s %s: %s\n", check.Level, check.Name, check.Message); err != nil {
+						return err
+					}
+				}
+			}
+
 			if failures > 0 {
 				return fmt.Errorf("doctor found %d failing check(s)", failures)
 			}
 			return nil
 		},
 	}
+	cmd.Flags().BoolVar(&asJSON, "json", false, "Output health checks as JSON")
+	return cmd
 }
 
 func (c *commandContext) runDoctor(ctx context.Context) []doctorCheck {
@@ -68,13 +89,7 @@ func (c *commandContext) runDoctor(ctx context.Context) []doctorCheck {
 		checks = append(checks, doctorCheck{Level: doctorPass, Name: "data-dir", Message: cfg.DataDir})
 	}
 
-	store, err := sqlite.Open(cfg.DataDir)
-	if err != nil {
-		checks = append(checks, doctorCheck{Level: doctorFail, Name: "sqlite", Message: err.Error()})
-	} else {
-		_ = store.Close()
-		checks = append(checks, doctorCheck{Level: doctorPass, Name: "sqlite", Message: "opened database and applied migrations"})
-	}
+	checks = append(checks, checkStore(cfg.DataDir))
 
 	st, err := c.inspectDaemon(ctx)
 	if err != nil {
@@ -103,6 +118,31 @@ func (c *commandContext) runDoctor(ctx context.Context) []doctorCheck {
 	return checks
 }
 
+// checkStore inspects the SQLite store WITHOUT opening or migrating it. The
+// daemon is the sole writer and migrator of the database (architecture.md §7);
+// the CLI must never run migrations or open a second writer against a database
+// a live daemon may already own. Migrations are validated by the daemon at
+// startup and surfaced through /readyz, so doctor only confirms whether the
+// database file exists yet.
+func checkStore(dataDir string) doctorCheck {
+	dbPath := filepath.Join(dataDir, "ao.db")
+	info, err := os.Stat(dbPath)
+	switch {
+	case err == nil:
+		return doctorCheck{
+			Level: doctorPass, Name: "sqlite",
+			Message: fmt.Sprintf("%s (%d bytes); migrations are applied by the daemon at startup", dbPath, info.Size()),
+		}
+	case errors.Is(err, fs.ErrNotExist):
+		return doctorCheck{
+			Level: doctorWarn, Name: "sqlite",
+			Message: "database not created yet; run `ao start` to initialize and migrate it",
+		}
+	default:
+		return doctorCheck{Level: doctorFail, Name: "sqlite", Message: err.Error()}
+	}
+}
+
 func (c *commandContext) checkTool(name string, required bool) doctorCheck {
 	path, err := c.deps.LookPath(name)
 	if err == nil {

backend/internal/cli/process.go

@@ -22,6 +22,10 @@ func startProcess(cfg processStartConfig) (processHandle, error) {
 	cmd.Env = cfg.Env
 	cmd.Stdout = cfg.Stdout
 	cmd.Stderr = cfg.Stderr
+	// Detach the daemon into its own session/process group so a Ctrl-C in the
+	// terminal where `ao start` is waiting for readiness doesn't also SIGINT the
+	// freshly spawned daemon (it would otherwise share the launcher's group).
+	cmd.SysProcAttr = detachSysProcAttr()
 	if err := cmd.Start(); err != nil {
 		return processHandle{}, err
 	}

backend/internal/cli/process_unix.go

@@ -14,3 +14,10 @@ func processAlive(pid int) bool {
 	err := syscall.Kill(pid, 0)
 	return err == nil || errors.Is(err, syscall.EPERM)
 }
+
+// detachSysProcAttr puts the daemon in a new session (Setsid) so it is no
+// longer in the launcher's foreground process group and won't receive the
+// terminal's SIGINT/SIGHUP.
+func detachSysProcAttr() *syscall.SysProcAttr {
+	return &syscall.SysProcAttr{Setsid: true}
+}

backend/internal/cli/process_windows.go

@@ -4,6 +4,7 @@ package cli
 
 import (
 	"errors"
+	"syscall"
 
 	"golang.org/x/sys/windows"
 )
@@ -27,3 +28,9 @@ func processAlive(pid int) bool {
 	}
 	return status == uint32(windows.WAIT_TIMEOUT)
 }
+
+// detachSysProcAttr starts the daemon in a new process group so it does not
+// receive the console's CTRL_C/CTRL_BREAK while `ao start` waits for readiness.
+func detachSysProcAttr() *syscall.SysProcAttr {
+	return &syscall.SysProcAttr{CreationFlags: windows.CREATE_NEW_PROCESS_GROUP}
+}

backend/internal/cli/root.go

@@ -3,6 +3,7 @@
 package cli
 
 import (
+	"errors"
 	"io"
 	"net/http"
 	"os"
@@ -19,6 +20,27 @@ func Execute() error {
 	return NewRootCommand(DefaultDeps()).Execute()
 }
 
+// usageError marks a command-line misuse (bad flag, wrong arg count). It lets
+// the process entrypoint return exit code 2 for usage errors versus 1 for
+// runtime failures, matching the convention CLIs are scripted against.
+type usageError struct{ err error }
+
+func (e usageError) Error() string { return e.err.Error() }
+func (e usageError) Unwrap() error { return e.err }
+
+// ExitCode maps a CLI error to a process exit code: 2 for usage errors, 1 for
+// any other failure, 0 for success.
+func ExitCode(err error) int {
+	if err == nil {
+		return 0
+	}
+	var ue usageError
+	if errors.As(err, &ue) {
+		return 2
+	}
+	return 1
+}
+
 // Deps holds the small set of side effects the CLI needs. Tests replace these
 // functions without reaching into process-global state.
 type Deps struct {
@@ -103,6 +125,11 @@ func NewRootCommand(deps Deps) *cobra.Command {
 	root.SetOut(deps.Out)
 	root.SetErr(deps.Err)
 	root.CompletionOptions.DisableDefaultCmd = true
+	// Tag flag-parse failures as usage errors so the entrypoint can exit 2 for
+	// misuse versus 1 for runtime failures. Subcommands inherit this func.
+	root.SetFlagErrorFunc(func(_ *cobra.Command, err error) error {
+		return usageError{err}
+	})
 
 	root.AddCommand(newDaemonCommand())
 	root.AddCommand(newStartCommand(ctx))

backend/internal/cli/stop.go

@@ -115,8 +115,14 @@ func (c *commandContext) waitForStopped(ctx context.Context, pid int, runFilePat
 			return daemonStatus{State: "stopped", RunFile: runFilePath, DataDir: dataDir}, nil
 		}
 		if !alive {
-			if err := runfile.Remove(runFilePath); err != nil {
-				return daemonStatus{}, err
+			// 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 err := runfile.Remove(runFilePath); err != nil {
+					return daemonStatus{}, err
+				}
 			}
 			return daemonStatus{State: "stopped", RunFile: runFilePath, DataDir: dataDir}, nil
 		}

backend/internal/cli/stop_test.go

@@ -0,0 +1,83 @@
+package cli
+
+import (
+	"context"
+	"path/filepath"
+	"testing"
+	"time"
+
+	"github.com/aoagents/agent-orchestrator/backend/internal/runfile"
+)
+
+// TestWaitForStoppedKeepsRunFileFromConcurrentStart guards against deleting a
+// fresh daemon's handshake: if a concurrent `ao start` replaces running.json
+// with a new live PID while we are polling the PID we stopped, waitForStopped
+// must report stopped but leave the new run-file intact.
+func TestWaitForStoppedKeepsRunFileFromConcurrentStart(t *testing.T) {
+	dir := t.TempDir()
+	runFile := filepath.Join(dir, "running.json")
+
+	const stoppedPID, newPID = 1111, 2222
+	// running.json now belongs to a different, live daemon.
+	if err := runfile.Write(runFile, runfile.Info{PID: newPID, Port: 3001, StartedAt: time.Unix(100, 0).UTC()}); err != nil {
+		t.Fatal(err)
+	}
+
+	c := &commandContext{deps: Deps{
+		ProcessAlive: func(pid int) bool { return pid == newPID }, // stoppedPID is dead
+		Now:          func() time.Time { return time.Unix(200, 0).UTC() },
+		Sleep:        func(time.Duration) {},
+	}.withDefaults()}
+
+	st, err := c.waitForStopped(context.Background(), stoppedPID, runFile, dir, time.Second)
+	if err != nil {
+		t.Fatal(err)
+	}
+	if st.State != "stopped" {
+		t.Fatalf("state = %q, want stopped", st.State)
+	}
+
+	info, err := runfile.Read(runFile)
+	if err != nil {
+		t.Fatal(err)
+	}
+	if info == nil {
+		t.Fatal("new daemon's run-file was deleted by stop of a different PID")
+	}
+	if info.PID != newPID {
+		t.Fatalf("run-file PID = %d, want %d (new daemon)", info.PID, newPID)
+	}
+}
+
+// TestWaitForStoppedRemovesOwnRunFile confirms the normal path still cleans up:
+// when the dead PID owns the run-file, it is removed.
+func TestWaitForStoppedRemovesOwnRunFile(t *testing.T) {
+	dir := t.TempDir()
+	runFile := filepath.Join(dir, "running.json")
+
+	const stoppedPID = 1111
+	if err := runfile.Write(runFile, runfile.Info{PID: stoppedPID, Port: 3001, StartedAt: time.Unix(100, 0).UTC()}); err != nil {
+		t.Fatal(err)
+	}
+
+	c := &commandContext{deps: Deps{
+		ProcessAlive: func(int) bool { return false },
+		Now:          func() time.Time { return time.Unix(200, 0).UTC() },
+		Sleep:        func(time.Duration) {},
+	}.withDefaults()}
+
+	st, err := c.waitForStopped(context.Background(), stoppedPID, runFile, dir, time.Second)
+	if err != nil {
+		t.Fatal(err)
+	}
+	if st.State != "stopped" {
+		t.Fatalf("state = %q, want stopped", st.State)
+	}
+	info, err := runfile.Read(runFile)
+	if err != nil {
+		t.Fatal(err)
+	}
+	if info != nil {
+		t.Fatalf("own run-file should have been removed, got %#v", info)
+	}
+}

backend/internal/daemon/daemon.go

@@ -27,7 +27,7 @@ func Run() error {
 		return err
 	}
 
-	log := NewLogger()
+	log := newLogger()
 
 	// Fail fast if a live daemon already owns the handshake file. A run-file
 	// left by a crashed predecessor (dead PID) is treated as stale and
@@ -119,8 +119,8 @@ func Run() error {
 	return runErr
 }
 
-// NewLogger returns the daemon's slog logger. It writes to stderr so supervisors
+// newLogger returns the daemon's slog logger. It writes to stderr so supervisors
 // can capture it separately from any structured stdout protocol added later.
-func NewLogger() *slog.Logger {
+func newLogger() *slog.Logger {
 	return slog.New(slog.NewTextHandler(os.Stderr, &slog.HandlerOptions{Level: slog.LevelDebug}))
 }

backend/internal/httpd/control_test.go

@@ -0,0 +1,52 @@
+package httpd
+
+import (
+	"net/http"
+	"net/http/httptest"
+	"testing"
+
+	"github.com/aoagents/agent-orchestrator/backend/internal/config"
+)
+
+// TestShutdownGuard verifies that POST /shutdown only fires for a trusted local
+// caller: a loopback Host with no Origin header. A cross-site Origin or a
+// non-loopback (DNS-rebinding) Host must be rejected without triggering the
+// shutdown side effect.
+func TestShutdownGuard(t *testing.T) {
+	cases := []struct {
+		name       string
+		host       string
+		origin     string
+		wantStatus int
+		wantFired  bool
+	}{
+		{name: "loopback no origin", host: "127.0.0.1:3001", wantStatus: http.StatusAccepted, wantFired: true},
+		{name: "localhost no origin", host: "localhost:3001", wantStatus: http.StatusAccepted, wantFired: true},
+		{name: "cross-site origin", host: "127.0.0.1:3001", origin: "https://evil.example", wantStatus: http.StatusForbidden, wantFired: false},
+		{name: "rebinding host", host: "evil.example", wantStatus: http.StatusForbidden, wantFired: false},
+	}
+
+	for _, tc := range cases {
+		t.Run(tc.name, func(t *testing.T) {
+			fired := false
+			r := NewRouterWithControl(config.Config{}, discardLogger(), nil, APIDeps{}, ControlDeps{
+				RequestShutdown: func() { fired = true },
+			})
+
+			req := httptest.NewRequest(http.MethodPost, "http://"+tc.host+"/shutdown", nil)
+			req.Host = tc.host
+			if tc.origin != "" {
+				req.Header.Set("Origin", tc.origin)
+			}
+			rec := httptest.NewRecorder()
+			r.ServeHTTP(rec, req)
+
+			if rec.Code != tc.wantStatus {
+				t.Fatalf("status = %d, want %d", rec.Code, tc.wantStatus)
+			}
+			if fired != tc.wantFired {
+				t.Fatalf("shutdown fired = %v, want %v", fired, tc.wantFired)
+			}
+		})
+	}
+}

backend/internal/httpd/router.go

@@ -6,6 +6,7 @@ package httpd
 
 import (
 	"log/slog"
+	"net"
 	"net/http"
 	"os"
 
@@ -76,11 +77,22 @@ func mountHealth(r chi.Router) {
 	r.Get("/readyz", handleReadyz)
 }
 
+// mountControl registers the loopback daemon-control endpoints. /shutdown is
+// unauthenticated and state-changing, so it is gated by localControlRequest to
+// keep a browser the user happens to have open (CSRF / DNS-rebinding) or a
+// remote client from being able to kill the daemon.
 func mountControl(r chi.Router, deps ControlDeps) {
 	if deps.RequestShutdown == nil {
 		return
 	}
-	r.Post("/shutdown", func(w http.ResponseWriter, _ *http.Request) {
+	r.Post("/shutdown", func(w http.ResponseWriter, req *http.Request) {
+		if !localControlRequest(req) {
+			writeJSON(w, http.StatusForbidden, map[string]any{
+				"status":  "forbidden",
+				"service": daemonmeta.ServiceName,
+			})
+			return
+		}
 		writeJSON(w, http.StatusAccepted, map[string]any{
 			"status":  "shutting_down",
 			"service": daemonmeta.ServiceName,
@@ -90,6 +102,29 @@ func mountControl(r chi.Router, deps ControlDeps) {
 	})
 }
 
+// localControlRequest reports whether a control request is a trusted local
+// caller. The Go CLI client addresses the daemon by its loopback host and
+// never sets an Origin header; a cross-site browser fetch always carries an
+// Origin, and a DNS-rebinding attempt resolves a non-loopback Host. Rejecting
+// either closes the CSRF/rebinding vector while leaving the CLI unaffected.
+func localControlRequest(r *http.Request) bool {
+	if r.Header.Get("Origin") != "" {
+		return false
+	}
+	host := r.Host
+	if h, _, err := net.SplitHostPort(host); err == nil {
+		host = h
+	}
+	switch host {
+	case "127.0.0.1", "::1", "localhost":
+		return true
+	}
+	if ip := net.ParseIP(host); ip != nil {
+		return ip.IsLoopback()
+	}
+	return false
+}
+
 // handleHealthz is the liveness probe: it answers 200 as long as the process is
 // up and serving. It does no dependency checks by design.
 func handleHealthz(w http.ResponseWriter, _ *http.Request) {

docs/cli/README.md

@@ -14,10 +14,13 @@ What works now:
 - `ao start` starts the daemon in the background and waits for `/readyz`.
 - `ao status` and `ao status --json` report stopped, stale, unhealthy,
   not-ready, or ready daemon state.
-- `ao stop` gracefully stops the daemon using the PID in `running.json`.
+- `ao stop` gracefully stops the daemon via the loopback `POST /shutdown`
+  endpoint, only after verifying the daemon's identity from `running.json`.
 - `ao daemon` is the hidden internal daemon entrypoint used by `ao start`.
-- `ao doctor` checks config, data dir, SQLite migrations, daemon state, and
-  local tool availability for `git`, `tmux`, and `zellij`.
+- `ao doctor` (and `ao doctor --json`) checks config, data dir, the database
+  file's presence, daemon state, and local tool availability for `git`, `tmux`,
+  and `zellij`. It never opens or migrates the store — the daemon is the sole
+  writer/migrator, so doctor only reports whether the database exists yet.
 - `ao completion` generates shell completions for `bash`, `zsh`, `fish`, and
   `powershell`.
 - `ao version` and `ao --version` print build metadata.
@@ -52,8 +55,9 @@ What is intentionally not implemented yet:
 
 Next steps:
 
-1. Add `/api/v1/projects` on the daemon over a small project service.
-2. Implement `ao project list/add/show/remove`.
+1. Wire the existing project manager/controller shell into the daemon with a
+   durable SQLite-backed project store.
+2. Implement `ao project list/add/show/remove` against `/api/v1/projects`.
 3. Wire production Session Manager dependencies: project-backed repo resolver,
    tmux/zellij runtime registry, first agent adapter, and AgentMessenger.
 4. Add `/api/v1/sessions`, then implement `ao spawn`, `ao session ...`, and
@@ -281,8 +285,8 @@ Acceptance criteria for the foundation:
 ## Implementation Readiness
 
 This section records what the CLI can connect to in the current codebase and
-what still needs to be built. Inventory date: 2026-05-31 on `main` at
-`0672dbb`.
+what still needs to be built. Inventory date: 2026-05-31 after merging
+`origin/main` at `438b830`.
 
 ### Implemented Foundation
 
@@ -298,8 +302,9 @@ Implemented commands:
   supports `--json` and `--timeout`.
 - `ao status` reports stopped/stale/unhealthy/not-ready/ready states and
   supports `--json`.
-- `ao doctor` checks config, data dir, SQLite open/migrations, daemon state, and
-  local tool availability for `git`, `tmux`, and `zellij`.
+- `ao doctor` checks config, data dir, database-file presence, daemon state, and
+  local tool availability for `git`, `tmux`, and `zellij`; supports `--json`. It
+  does not open or migrate the store (the daemon owns that).
 - `ao completion` generates `bash`, `zsh`, `fish`, and `powershell`
   completions.
 - `ao version` prints build metadata.
@@ -331,7 +336,7 @@ they are wired into the daemon and exposed through HTTP.
 
 | Area | Existing code | Missing before CLI can use it |
 |---|---|---|
-| Project persistence | `sqlite.Store` has `UpsertProject`, `GetProject`, `ListProjects`, and `ArchiveProject`. | Project domain/service layer, project ID/path/origin validation, and `/api/v1/projects` routes. |
+| Project API pieces | `internal/project` has manager/controller DTOs, `/api/v1/projects` routes exist, and `sqlite.Store` has project CRUD. | Durable project-store adapter/wiring in the daemon and CLI commands. The daemon currently constructs the router with nil API deps, so project routes are not product-usable from `ao` yet. |
 | Session Manager | `backend/internal/session.Manager` implements `Spawn`, `Kill`, `Restore`, `List`, `Get`, `Send`, and `Cleanup`. | Production daemon wiring with real runtime, agent, workspace, messenger, and HTTP routes. |
 | Runtime adapters | tmux and zellij adapters implement `ports.Runtime` and also have attach/send/output helpers. | Runtime registry wiring in daemon, attach/send abstractions in ports/API, and selection config. |
 | Workspace adapter | git worktree adapter implements create/destroy/restore/list with safety checks. | Repo resolver backed by registered projects and daemon wiring into Session Manager. |
@@ -345,12 +350,10 @@ These are the main gaps before the full initial command set is real.
 
 | Gap | Blocks |
 |---|---|
-| Cobra dependency and CLI packages. | All CLI commands. |
-| Daemon extraction from `backend/main.go` into `internal/daemon`. | `ao daemon`, `ao start`, tests around daemon startup. |
-| CLI process runner and PID signal helpers. | `ao start`, `ao stop`. |
-| Loopback HTTP client package with run-file discovery. | `ao status`, later all daemon-backed commands. |
+| Product API client package with run-file discovery. | `project`, `spawn`, `session`, `send`, `events list`, richer `status`. |
 | Shutdown mechanism choice: PID signal now, optional `POST /api/v1/daemon/shutdown` later. | `ao stop` polish and cross-platform behavior. |
-| HTTP API route surface under `/api/v1`. | `project`, `spawn`, `session`, `send`, `events list`, richer `status`. |
+| Session/send API route surface under `/api/v1`. | `spawn`, `session`, `send`, richer `status`. |
+| Project API daemon wiring. | `ao project list/add/show/remove`. |
 | SSE route for live CDC events plus durable catch-up reads. | `ao events tail`, frontend live updates. |
 | Agent adapters for supported harnesses (`codex`, `claude-code`, etc.). | `ao spawn`, `ao session restore`. |
 | AgentMessenger implementation over tmux/zellij. | `ao send`, LCM auto-nudge reactions. |
@@ -368,10 +371,10 @@ These are the main gaps before the full initial command set is real.
 | `ao start` | Implemented | Config, run-file stale check, HTTP readiness probes. | Later: package-manager/service integration if needed. |
 | `ao stop` | Implemented | Run-file discovery gives PID/port; server exits cleanly on SIGINT/SIGTERM. | Optional later shutdown HTTP route. |
 | `ao status` | Partially implemented | Run-file, process liveness via PID, `/healthz`, `/readyz`. | Rich project/session summary waits for `/api/v1/projects` and `/api/v1/sessions`. |
-| `ao doctor` | Partially implemented | Config resolution, run-file, storage open, runtime binary checks. | Deeper adapter preflights need daemon wiring/config. |
+| `ao doctor` | Partially implemented | Config resolution, run-file, database-file presence (no open/migrate), runtime binary checks. | Deeper adapter preflights need daemon wiring/config and should be queried from the daemon, not run in-process. |
 | `ao completion` | Implemented | Cobra generators. | None for foundation. |
 | `ao version` | Implemented | Build metadata can be injected with `-ldflags`. | Release tooling needs to set metadata. |
-| `ao project list/add/show/remove` | Not yet | SQLite project CRUD exists. | Project service and HTTP routes. CLI must not write SQLite directly. |
+| `ao project list/add/show/remove` | Not yet | Project manager/controller route shell and SQLite project CRUD exist. | Durable project-store adapter, daemon API wiring, and CLI HTTP client. CLI must not write SQLite directly. |
 | `ao spawn` | Not yet | Session Manager exists; runtime/workspace/tracker pieces partly exist. | Agent adapters, registry/config wiring, project lookup, tracker hydration, HTTP route. |
 | `ao session list/show` | Not yet | Store and Session Manager read model exist. | HTTP routes and response DTOs. |
 | `ao session attach` | Not yet | tmux/zellij have attach command helpers. | Runtime attach port/API and terminal-launch policy. |
@@ -383,8 +386,8 @@ These are the main gaps before the full initial command set is real.
 
 1. Build CLI foundation around the daemon only: `daemon`, `start`, `stop`,
    `status`, `doctor`, `completion`, `version`.
-2. Add `/api/v1/projects` over a small project service, then implement
-   `project list/add/show/remove`.
+2. Wire the existing project manager/controller shell into the daemon with a
+   durable SQLite-backed store, then implement `project list/add/show/remove`.
 3. Wire production Session Manager dependencies: project-backed repo resolver,
    tmux/zellij runtime registry, first agent adapter, and AgentMessenger.
 4. Add `/api/v1/sessions` and implement `spawn`, `session list/show/kill/restore`,