Merge branch 'fix/multi-repo-routing-pr811-v2'

internal/.events.jsonl

@@ -0,0 +1,5 @@
+{"ts":"2026-01-18T09:52:29Z","source":"gt","type":"session_death","actor":"gt-gastown-witness","payload":{"agent":"unknown","caller":"gt doctor","reason":"zombie cleanup","session":"gt-gastown-witness"},"visibility":"feed"}
+{"ts":"2026-01-18T10:00:24Z","source":"gt","type":"session_death","actor":"gt-gastown-witness","payload":{"agent":"unknown","caller":"gt doctor","reason":"zombie cleanup","session":"gt-gastown-witness"},"visibility":"feed"}
+{"ts":"2026-01-18T10:06:48Z","source":"gt","type":"session_death","actor":"gt-gastown-witness","payload":{"agent":"unknown","caller":"gt doctor","reason":"zombie cleanup","session":"gt-gastown-witness"},"visibility":"feed"}
+{"ts":"2026-01-18T14:26:38Z","source":"gt","type":"session_death","actor":"gt-gastown-witness","payload":{"agent":"unknown","caller":"gt doctor","reason":"zombie cleanup","session":"gt-gastown-witness"},"visibility":"feed"}
+{"ts":"2026-01-18T14:30:02Z","source":"gt","type":"session_death","actor":"gt-gastown-witness","payload":{"agent":"unknown","caller":"gt doctor","reason":"zombie cleanup","session":"gt-gastown-witness"},"visibility":"feed"}

internal/beads/beads.go

@@ -114,6 +114,11 @@ type Beads struct {
 	workDir  string
 	beadsDir string // Optional BEADS_DIR override for cross-database access
 	isolated bool   // If true, suppress inherited beads env vars (for test isolation)
+
+	// Lazy-cached town root for routing resolution.
+	// Populated on first call to getTownRoot() to avoid filesystem walk on every operation.
+	townRoot     string
+	searchedRoot bool
 }
 
 // New creates a new Beads wrapper for the given directory.
@@ -144,6 +149,26 @@ func (b *Beads) getActor() string {
 	return os.Getenv("BD_ACTOR")
 }
 
+// getTownRoot returns the Gas Town root directory, using lazy caching.
+// The town root is found by walking up from workDir looking for mayor/town.json.
+// Returns empty string if not in a Gas Town project.
+func (b *Beads) getTownRoot() string {
+	if !b.searchedRoot {
+		b.townRoot = FindTownRoot(b.workDir)
+		b.searchedRoot = true
+	}
+	return b.townRoot
+}
+
+// getResolvedBeadsDir returns the beads directory this wrapper is operating on.
+// This follows any redirects and returns the actual beads directory path.
+func (b *Beads) getResolvedBeadsDir() string {
+	if b.beadsDir != "" {
+		return b.beadsDir
+	}
+	return ResolveBeadsDir(b.workDir)
+}
+
 // Init initializes a new beads database in the working directory.
 // This uses the same environment isolation as other commands.
 func (b *Beads) Init(prefix string) error {

internal/beads/beads_agent.go

@@ -5,9 +5,32 @@ import (
 	"encoding/json"
 	"errors"
 	"fmt"
+	"os/exec"
 	"strings"
 )
 
+// runSlotSet runs `bd slot set` from a specific directory.
+// This is needed when the agent bead was created via routing to a different
+// database than the Beads wrapper's default directory.
+func runSlotSet(workDir, beadID, slotName, slotValue string) error {
+	cmd := exec.Command("bd", "slot", "set", beadID, slotName, slotValue)
+	cmd.Dir = workDir
+	if output, err := cmd.CombinedOutput(); err != nil {
+		return fmt.Errorf("%s: %w", strings.TrimSpace(string(output)), err)
+	}
+	return nil
+}
+
+// runSlotClear runs `bd slot clear` from a specific directory.
+func runSlotClear(workDir, beadID, slotName string) error {
+	cmd := exec.Command("bd", "slot", "clear", beadID, slotName)
+	cmd.Dir = workDir
+	if output, err := cmd.CombinedOutput(); err != nil {
+		return fmt.Errorf("%s: %w", strings.TrimSpace(string(output)), err)
+	}
+	return nil
+}
+
 // AgentFields holds structured fields for agent beads.
 // These are stored as "key: value" lines in the description.
 type AgentFields struct {
@@ -125,7 +148,21 @@ func ParseAgentFields(description string) *AgentFields {
 // The ID format is: <prefix>-<rig>-<role>-<name> (e.g., gt-gastown-polecat-Toast)
 // Use AgentBeadID() helper to generate correct IDs.
 // The created_by field is populated from BD_ACTOR env var for provenance tracking.
+//
+// This function automatically ensures custom types are configured in the target
+// database before creating the bead. This handles multi-repo routing scenarios
+// where the bead may be routed to a different database than the one this wrapper
+// is connected to.
 func (b *Beads) CreateAgentBead(id, title string, fields *AgentFields) (*Issue, error) {
+	// Resolve where this bead will actually be written (handles multi-repo routing)
+	targetDir := ResolveRoutingTarget(b.getTownRoot(), id, b.getResolvedBeadsDir())
+
+	// Ensure target database has custom types configured
+	// This is cached (sentinel file + in-memory) so repeated calls are fast
+	if err := EnsureCustomTypes(targetDir); err != nil {
+		return nil, fmt.Errorf("prepare target for agent bead %s: %w", id, err)
+	}
+
 	description := FormatAgentDescription(title, fields)
 
 	args := []string{"create", "--json",
@@ -160,8 +197,9 @@ func (b *Beads) CreateAgentBead(id, title string, fields *AgentFields) (*Issue,
 	// Set the hook slot if specified (this is the authoritative storage)
 	// This fixes the slot inconsistency bug where bead status is 'hooked' but
 	// agent's hook slot is empty. See mi-619.
+	// Must run from targetDir since that's where the agent bead was created
 	if fields != nil && fields.HookBead != "" {
-		if _, err := b.run("slot", "set", id, "hook", fields.HookBead); err != nil {
+		if err := runSlotSet(targetDir, id, "hook", fields.HookBead); err != nil {
 			// Non-fatal: warn but continue - description text has the backup
 			fmt.Printf("Warning: could not set hook slot: %v\n", err)
 		}
@@ -195,6 +233,9 @@ func (b *Beads) CreateOrReopenAgentBead(id, title string, fields *AgentFields) (
 		return nil, err
 	}
 
+	// Resolve where this bead lives (for slot operations)
+	targetDir := ResolveRoutingTarget(b.getTownRoot(), id, b.getResolvedBeadsDir())
+
 	// The bead already exists (should be closed from previous polecat lifecycle)
 	// Reopen it and update its fields
 	if _, reopenErr := b.run("reopen", id, "--reason=re-spawning agent"); reopenErr != nil {
@@ -217,12 +258,14 @@ func (b *Beads) CreateOrReopenAgentBead(id, title string, fields *AgentFields) (
 	// Note: role slot no longer set - role definitions are config-based
 
 	// Clear any existing hook slot (handles stale state from previous lifecycle)
-	_, _ = b.run("slot", "clear", id, "hook")
+	// Must run from targetDir since that's where the agent bead lives
+	_ = runSlotClear(targetDir, id, "hook")
 
 	// Set the hook slot if specified
+	// Must run from targetDir since that's where the agent bead lives
 	if fields != nil && fields.HookBead != "" {
-		if _, err := b.run("slot", "set", id, "hook", fields.HookBead); err != nil {
-			// Non-fatal: warn but continue
+		if err := runSlotSet(targetDir, id, "hook", fields.HookBead); err != nil {
+			// Non-fatal: warn but continue - description text has the backup
 			fmt.Printf("Warning: could not set hook slot: %v\n", err)
 		}
 	}

internal/beads/beads_types.go

@@ -0,0 +1,129 @@
+// Package beads provides custom type management for agent beads.
+package beads
+
+import (
+	"fmt"
+	"os"
+	"os/exec"
+	"path/filepath"
+	"strings"
+	"sync"
+
+	"github.com/steveyegge/gastown/internal/constants"
+)
+
+// typesSentinel is a marker file indicating custom types have been configured.
+// This persists across CLI invocations to avoid redundant bd config calls.
+const typesSentinel = ".gt-types-configured"
+
+// ensuredDirs tracks which beads directories have been ensured this session.
+// This provides fast in-memory caching for multiple creates in the same CLI run.
+var (
+	ensuredDirs = make(map[string]bool)
+	ensuredMu   sync.Mutex
+)
+
+// FindTownRoot walks up from startDir to find the Gas Town root directory.
+// The town root is identified by the presence of mayor/town.json.
+// Returns empty string if not found (reached filesystem root).
+func FindTownRoot(startDir string) string {
+	dir := startDir
+	for {
+		townFile := filepath.Join(dir, "mayor", "town.json")
+		if _, err := os.Stat(townFile); err == nil {
+			return dir
+		}
+		parent := filepath.Dir(dir)
+		if parent == dir {
+			return "" // Reached filesystem root
+		}
+		dir = parent
+	}
+}
+
+// ResolveRoutingTarget determines which beads directory a bead ID will route to.
+// It extracts the prefix from the bead ID and looks up the corresponding route.
+// Returns the resolved beads directory path, following any redirects.
+//
+// If townRoot is empty or prefix is not found, falls back to the provided fallbackDir.
+func ResolveRoutingTarget(townRoot, beadID, fallbackDir string) string {
+	if townRoot == "" {
+		return fallbackDir
+	}
+
+	// Extract prefix from bead ID (e.g., "gt-gastown-polecat-Toast" -> "gt-")
+	prefix := ExtractPrefix(beadID)
+	if prefix == "" {
+		return fallbackDir
+	}
+
+	// Look up rig path for this prefix
+	rigPath := GetRigPathForPrefix(townRoot, prefix)
+	if rigPath == "" {
+		return fallbackDir
+	}
+
+	// Resolve redirects and get final beads directory
+	beadsDir := ResolveBeadsDir(rigPath)
+	if beadsDir == "" {
+		return fallbackDir
+	}
+
+	return beadsDir
+}
+
+// EnsureCustomTypes ensures the target beads directory has custom types configured.
+// Uses a two-level caching strategy:
+//   - In-memory cache for multiple creates in the same CLI invocation
+//   - Sentinel file on disk for persistence across CLI invocations
+//
+// This function is thread-safe and idempotent.
+func EnsureCustomTypes(beadsDir string) error {
+	if beadsDir == "" {
+		return fmt.Errorf("empty beads directory")
+	}
+
+	ensuredMu.Lock()
+	defer ensuredMu.Unlock()
+
+	// Fast path: in-memory cache (same CLI invocation)
+	if ensuredDirs[beadsDir] {
+		return nil
+	}
+
+	// Fast path: sentinel file exists (previous CLI invocation)
+	sentinelPath := filepath.Join(beadsDir, typesSentinel)
+	if _, err := os.Stat(sentinelPath); err == nil {
+		ensuredDirs[beadsDir] = true
+		return nil
+	}
+
+	// Verify beads directory exists
+	if _, err := os.Stat(beadsDir); os.IsNotExist(err) {
+		return fmt.Errorf("beads directory does not exist: %s", beadsDir)
+	}
+
+	// Configure custom types via bd CLI
+	typesList := strings.Join(constants.BeadsCustomTypesList(), ",")
+	cmd := exec.Command("bd", "config", "set", "types.custom", typesList)
+	cmd.Dir = beadsDir
+	if output, err := cmd.CombinedOutput(); err != nil {
+		return fmt.Errorf("configure custom types in %s: %s: %w",
+			beadsDir, strings.TrimSpace(string(output)), err)
+	}
+
+	// Write sentinel file (best effort - don't fail if this fails)
+	// The sentinel contains a version marker for future compatibility
+	_ = os.WriteFile(sentinelPath, []byte("v1\n"), 0644)
+
+	ensuredDirs[beadsDir] = true
+	return nil
+}
+
+// ResetEnsuredDirs clears the in-memory cache of ensured directories.
+// This is primarily useful for testing.
+func ResetEnsuredDirs() {
+	ensuredMu.Lock()
+	defer ensuredMu.Unlock()
+	ensuredDirs = make(map[string]bool)
+}

internal/beads/beads_types_test.go

@@ -0,0 +1,234 @@
+package beads
+
+import (
+	"os"
+	"path/filepath"
+	"testing"
+)
+
+func TestFindTownRoot(t *testing.T) {
+	// Create a temporary town structure
+	tmpDir := t.TempDir()
+	mayorDir := filepath.Join(tmpDir, "mayor")
+	if err := os.MkdirAll(mayorDir, 0755); err != nil {
+		t.Fatal(err)
+	}
+	if err := os.WriteFile(filepath.Join(mayorDir, "town.json"), []byte("{}"), 0644); err != nil {
+		t.Fatal(err)
+	}
+
+	// Create nested directories
+	deepDir := filepath.Join(tmpDir, "rig1", "crew", "worker1")
+	if err := os.MkdirAll(deepDir, 0755); err != nil {
+		t.Fatal(err)
+	}
+
+	tests := []struct {
+		name     string
+		startDir string
+		expected string
+	}{
+		{"from town root", tmpDir, tmpDir},
+		{"from mayor dir", mayorDir, tmpDir},
+		{"from deep nested dir", deepDir, tmpDir},
+		{"from non-town dir", t.TempDir(), ""},
+	}
+
+	for _, tc := range tests {
+		t.Run(tc.name, func(t *testing.T) {
+			result := FindTownRoot(tc.startDir)
+			if result != tc.expected {
+				t.Errorf("FindTownRoot(%q) = %q, want %q", tc.startDir, result, tc.expected)
+			}
+		})
+	}
+}
+
+func TestResolveRoutingTarget(t *testing.T) {
+	// Create a temporary town with routes
+	tmpDir := t.TempDir()
+	beadsDir := filepath.Join(tmpDir, ".beads")
+	if err := os.MkdirAll(beadsDir, 0755); err != nil {
+		t.Fatal(err)
+	}
+
+	// Create mayor/town.json for FindTownRoot
+	mayorDir := filepath.Join(tmpDir, "mayor")
+	if err := os.MkdirAll(mayorDir, 0755); err != nil {
+		t.Fatal(err)
+	}
+	if err := os.WriteFile(filepath.Join(mayorDir, "town.json"), []byte("{}"), 0644); err != nil {
+		t.Fatal(err)
+	}
+
+	// Create routes.jsonl
+	routesContent := `{"prefix": "gt-", "path": "gastown/mayor/rig"}
+{"prefix": "hq-", "path": "."}
+`
+	if err := os.WriteFile(filepath.Join(beadsDir, "routes.jsonl"), []byte(routesContent), 0644); err != nil {
+		t.Fatal(err)
+	}
+
+	// Create the rig beads directory
+	rigBeadsDir := filepath.Join(tmpDir, "gastown", "mayor", "rig", ".beads")
+	if err := os.MkdirAll(rigBeadsDir, 0755); err != nil {
+		t.Fatal(err)
+	}
+
+	fallback := "/fallback/.beads"
+
+	tests := []struct {
+		name     string
+		townRoot string
+		beadID   string
+		expected string
+	}{
+		{
+			name:     "rig-level bead routes to rig",
+			townRoot: tmpDir,
+			beadID:   "gt-gastown-polecat-Toast",
+			expected: rigBeadsDir,
+		},
+		{
+			name:     "town-level bead routes to town",
+			townRoot: tmpDir,
+			beadID:   "hq-mayor",
+			expected: beadsDir,
+		},
+		{
+			name:     "unknown prefix falls back",
+			townRoot: tmpDir,
+			beadID:   "xx-unknown",
+			expected: fallback,
+		},
+		{
+			name:     "empty townRoot falls back",
+			townRoot: "",
+			beadID:   "gt-gastown-polecat-Toast",
+			expected: fallback,
+		},
+		{
+			name:     "no prefix falls back",
+			townRoot: tmpDir,
+			beadID:   "noprefixid",
+			expected: fallback,
+		},
+	}
+
+	for _, tc := range tests {
+		t.Run(tc.name, func(t *testing.T) {
+			result := ResolveRoutingTarget(tc.townRoot, tc.beadID, fallback)
+			if result != tc.expected {
+				t.Errorf("ResolveRoutingTarget(%q, %q, %q) = %q, want %q",
+					tc.townRoot, tc.beadID, fallback, result, tc.expected)
+			}
+		})
+	}
+}
+
+func TestEnsureCustomTypes(t *testing.T) {
+	// Reset the in-memory cache before testing
+	ResetEnsuredDirs()
+
+	t.Run("empty beads dir returns error", func(t *testing.T) {
+		err := EnsureCustomTypes("")
+		if err == nil {
+			t.Error("expected error for empty beads dir")
+		}
+	})
+
+	t.Run("non-existent beads dir returns error", func(t *testing.T) {
+		err := EnsureCustomTypes("/nonexistent/path/.beads")
+		if err == nil {
+			t.Error("expected error for non-existent beads dir")
+		}
+	})
+
+	t.Run("sentinel file triggers cache hit", func(t *testing.T) {
+		tmpDir := t.TempDir()
+		beadsDir := filepath.Join(tmpDir, ".beads")
+		if err := os.MkdirAll(beadsDir, 0755); err != nil {
+			t.Fatal(err)
+		}
+
+		// Create sentinel file
+		sentinelPath := filepath.Join(beadsDir, typesSentinel)
+		if err := os.WriteFile(sentinelPath, []byte("v1\n"), 0644); err != nil {
+			t.Fatal(err)
+		}
+
+		// Reset cache to ensure we're testing sentinel detection
+		ResetEnsuredDirs()
+
+		// This should succeed without running bd (sentinel exists)
+		err := EnsureCustomTypes(beadsDir)
+		if err != nil {
+			t.Errorf("expected success with sentinel file, got: %v", err)
+		}
+	})
+
+	t.Run("in-memory cache prevents repeated calls", func(t *testing.T) {
+		tmpDir := t.TempDir()
+		beadsDir := filepath.Join(tmpDir, ".beads")
+		if err := os.MkdirAll(beadsDir, 0755); err != nil {
+			t.Fatal(err)
+		}
+
+		// Create sentinel to avoid bd call
+		sentinelPath := filepath.Join(beadsDir, typesSentinel)
+		if err := os.WriteFile(sentinelPath, []byte("v1\n"), 0644); err != nil {
+			t.Fatal(err)
+		}
+
+		ResetEnsuredDirs()
+
+		// First call
+		if err := EnsureCustomTypes(beadsDir); err != nil {
+			t.Fatal(err)
+		}
+
+		// Remove sentinel - second call should still succeed due to in-memory cache
+		os.Remove(sentinelPath)
+
+		if err := EnsureCustomTypes(beadsDir); err != nil {
+			t.Errorf("expected cache hit, got: %v", err)
+		}
+	})
+}
+
+func TestBeads_getTownRoot(t *testing.T) {
+	// Create a temporary town
+	tmpDir := t.TempDir()
+	mayorDir := filepath.Join(tmpDir, "mayor")
+	if err := os.MkdirAll(mayorDir, 0755); err != nil {
+		t.Fatal(err)
+	}
+	if err := os.WriteFile(filepath.Join(mayorDir, "town.json"), []byte("{}"), 0644); err != nil {
+		t.Fatal(err)
+	}
+
+	// Create nested directory
+	rigDir := filepath.Join(tmpDir, "myrig", "mayor", "rig")
+	if err := os.MkdirAll(rigDir, 0755); err != nil {
+		t.Fatal(err)
+	}
+
+	b := New(rigDir)
+
+	// First call should find town root
+	root1 := b.getTownRoot()
+	if root1 != tmpDir {
+		t.Errorf("first getTownRoot() = %q, want %q", root1, tmpDir)
+	}
+
+	// Second call should return cached value
+	root2 := b.getTownRoot()
+	if root2 != root1 {
+		t.Errorf("second getTownRoot() = %q, want cached %q", root2, root1)
+	}
+
+	// Verify searchedRoot flag is set
+	if !b.searchedRoot {
+		t.Error("expected searchedRoot to be true after getTownRoot()")
+	}
+}

internal/claude/config/settings-autonomous.json

@@ -38,7 +38,7 @@
         "hooks": [
           {
             "type": "command",
-            "command": "export PATH=\"$HOME/go/bin:$HOME/bin:$PATH\" && gt prime && gt mail check --inject && gt nudge deacon session-started"
+            "command": "export PATH=\"$HOME/go/bin:$HOME/bin:$PATH\" && gt prime --hook && gt mail check --inject && gt nudge deacon session-started"
           }
         ]
       }
@@ -49,7 +49,7 @@
         "hooks": [
           {
             "type": "command",
-            "command": "export PATH=\"$HOME/go/bin:$HOME/bin:$PATH\" && gt prime"
+            "command": "export PATH=\"$HOME/go/bin:$HOME/bin:$PATH\" && gt prime --hook"
           }
         ]
       }

internal/claude/config/settings-interactive.json

@@ -38,7 +38,7 @@
         "hooks": [
           {
             "type": "command",
-            "command": "export PATH=\"$HOME/go/bin:$HOME/bin:$PATH\" && gt prime && gt nudge deacon session-started"
+            "command": "export PATH=\"$HOME/go/bin:$HOME/bin:$PATH\" && gt prime --hook && gt nudge deacon session-started"
           }
         ]
       }
@@ -49,7 +49,7 @@
         "hooks": [
           {
             "type": "command",
-            "command": "export PATH=\"$HOME/go/bin:$HOME/bin:$PATH\" && gt prime"
+            "command": "export PATH=\"$HOME/go/bin:$HOME/bin:$PATH\" && gt prime --hook"
           }
         ]
       }

internal/cmd/gitinit.go

@@ -138,6 +138,11 @@ func runGitInit(cmd *cobra.Command, args []string) error {
 		fmt.Printf("   ✓ Git repository already exists\n")
 	}
 
+	// Install pre-checkout hook to prevent accidental branch switches
+	if err := InstallPreCheckoutHook(hqRoot); err != nil {
+		fmt.Printf("   %s Could not install pre-checkout hook: %v\n", style.Dim.Render("⚠"), err)
+	}
+
 	// Create GitHub repo if requested
 	if gitInitGitHub != "" {
 		if err := createGitHubRepo(hqRoot, gitInitGitHub, !gitInitPublic); err != nil {

internal/cmd/install.go

@@ -221,6 +221,30 @@ func runInstall(cmd *cobra.Command, args []string) error {
 		fmt.Printf("   ✓ Created deacon/.claude/settings.json\n")
 	}
 
+	// Create boot directory (deacon/dogs/boot/) for Boot watchdog.
+	// This avoids gt doctor warning on fresh install.
+	bootDir := filepath.Join(deaconDir, "dogs", "boot")
+	if err := os.MkdirAll(bootDir, 0755); err != nil {
+		fmt.Printf("   %s Could not create boot directory: %v\n", style.Dim.Render("⚠"), err)
+	}
+
+	// Create plugins directory for town-level patrol plugins.
+	// This avoids gt doctor warning on fresh install.
+	pluginsDir := filepath.Join(absPath, "plugins")
+	if err := os.MkdirAll(pluginsDir, 0755); err != nil {
+		fmt.Printf("   %s Could not create plugins directory: %v\n", style.Dim.Render("⚠"), err)
+	} else {
+		fmt.Printf("   ✓ Created plugins/\n")
+	}
+
+	// Create daemon.json patrol config.
+	// This avoids gt doctor warning on fresh install.
+	if err := config.EnsureDaemonPatrolConfig(absPath); err != nil {
+		fmt.Printf("   %s Could not create daemon.json: %v\n", style.Dim.Render("⚠"), err)
+	} else {
+		fmt.Printf("   ✓ Created mayor/daemon.json\n")
+	}
+
 	// Initialize git BEFORE beads so that bd can compute repository fingerprint.
 	// The fingerprint is required for the daemon to start properly.
 	if installGit || installGitHub != "" {
@@ -234,6 +258,12 @@ func runInstall(cmd *cobra.Command, args []string) error {
 	// Town beads (hq- prefix) stores mayor mail, cross-rig coordination, and handoffs.
 	// Rig beads are separate and have their own prefixes.
 	if !installNoBeads {
+		// Kill any orphaned bd daemons before initializing beads.
+		// Stale daemons can interfere with fresh database creation.
+		if killed, _, _ := beads.StopAllBdProcesses(false, true); killed > 0 {
+			fmt.Printf("   ✓ Stopped %d orphaned bd daemon(s)\n", killed)
+		}
+
 		if err := initTownBeads(absPath); err != nil {
 			fmt.Printf("   %s Could not initialize town beads: %v\n", style.Dim.Render("⚠"), err)
 		} else {
@@ -369,6 +399,19 @@ func initTownBeads(townPath string) error {
 		}
 	}
 
+	// Verify .beads directory was actually created (bd init can exit 0 without creating it)
+	beadsDir := filepath.Join(townPath, ".beads")
+	if _, statErr := os.Stat(beadsDir); os.IsNotExist(statErr) {
+		return fmt.Errorf("bd init succeeded but .beads directory not created (check bd daemon interference)")
+	}
+
+	// Explicitly set issue_prefix config (bd init --prefix may not persist it in newer versions).
+	prefixSetCmd := exec.Command("bd", "config", "set", "issue_prefix", "hq")
+	prefixSetCmd.Dir = townPath
+	if prefixOutput, prefixErr := prefixSetCmd.CombinedOutput(); prefixErr != nil {
+		return fmt.Errorf("bd config set issue_prefix failed: %s", strings.TrimSpace(string(prefixOutput)))
+	}
+
 	// Configure custom types for Gas Town (agent, role, rig, convoy, slot).
 	// These were extracted from beads core in v0.46.0 and now require explicit config.
 	configCmd := exec.Command("bd", "config", "set", "types.custom", constants.BeadsCustomTypes)
@@ -468,7 +511,7 @@ func initTownAgentBeads(townPath string) error {
 	// bd init doesn't enable "custom" issue types by default, but Gas Town uses
 	// agent beads during install and runtime. Ensure these types are enabled
 	// before attempting to create any town-level system beads.
-	if err := ensureBeadsCustomTypes(townPath, []string{"agent", "rig", "convoy", "slot"}); err != nil {
+	if err := ensureBeadsCustomTypes(townPath, constants.BeadsCustomTypesList()); err != nil {
 		return err
 	}
 

internal/doctor/boot_check.go

@@ -11,20 +11,37 @@ import (
 // BootHealthCheck verifies Boot watchdog health.
 // "The vet checks on the dog."
 type BootHealthCheck struct {
-	BaseCheck
+	FixableCheck
+	missingDir bool // track if directory is missing for Fix()
 }
 
 // NewBootHealthCheck creates a new Boot health check.
 func NewBootHealthCheck() *BootHealthCheck {
 	return &BootHealthCheck{
-		BaseCheck: BaseCheck{
-			CheckName:        "boot-health",
-			CheckDescription: "Check Boot watchdog health (the vet checks on the dog)",
-			CheckCategory:    CategoryInfrastructure,
+		FixableCheck: FixableCheck{
+			BaseCheck: BaseCheck{
+				CheckName:        "boot-health",
+				CheckDescription: "Check Boot watchdog health (the vet checks on the dog)",
+				CheckCategory:    CategoryInfrastructure,
+			},
 		},
 	}
 }
 
+// CanFix returns true only if the directory is missing (we can create it).
+func (c *BootHealthCheck) CanFix() bool {
+	return c.missingDir
+}
+
+// Fix creates the missing boot directory.
+func (c *BootHealthCheck) Fix(ctx *CheckContext) error {
+	if !c.missingDir {
+		return nil
+	}
+	b := boot.New(ctx.TownRoot)
+	return b.EnsureDir()
+}
+
 // Run checks Boot health: directory, session, status, and marker freshness.
 func (c *BootHealthCheck) Run(ctx *CheckContext) *CheckResult {
 	b := boot.New(ctx.TownRoot)
@@ -33,12 +50,13 @@ func (c *BootHealthCheck) Run(ctx *CheckContext) *CheckResult {
 	// Check 1: Boot directory exists
 	bootDir := b.Dir()
 	if _, err := os.Stat(bootDir); os.IsNotExist(err) {
+		c.missingDir = true
 		return &CheckResult{
 			Name:    c.Name(),
 			Status:  StatusWarning,
 			Message: "Boot directory not present",
 			Details: []string{fmt.Sprintf("Expected: %s", bootDir)},
-			FixHint: "Boot directory is created on first daemon run",
+			FixHint: "Run 'gt doctor --fix' to create it",
 		}
 	}
 

internal/doctor/patrol_check.go

@@ -458,11 +458,20 @@ func (c *PatrolRolesHavePromptsCheck) Run(ctx *CheckContext) *CheckResult {
 	}
 
 	var missingPrompts []string
+	rigsChecked := 0
 	for _, rigName := range rigs {
 		// Check in mayor's clone (canonical for the rig)
 		mayorRig := filepath.Join(ctx.TownRoot, rigName, "mayor", "rig")
 		templatesDir := filepath.Join(mayorRig, "internal", "templates", "roles")
 
+		// Skip rigs that don't have internal/templates structure.
+		// Most repos won't have this - templates are embedded in gastown binary.
+		// Only check rigs that explicitly have their own template overrides.
+		if _, err := os.Stat(filepath.Join(mayorRig, "internal", "templates")); os.IsNotExist(err) {
+			continue
+		}
+		rigsChecked++
+
 		var rigMissing []string
 		for _, roleFile := range requiredRolePrompts {
 			promptPath := filepath.Join(templatesDir, roleFile)
@@ -476,13 +485,21 @@ func (c *PatrolRolesHavePromptsCheck) Run(ctx *CheckContext) *CheckResult {
 		}
 	}
 
+	// Templates are embedded in gastown binary - missing files in rig repos is normal.
+	// Only report as informational, not a warning.
+	if rigsChecked == 0 {
+		return &CheckResult{
+			Name:    c.Name(),
+			Status:  StatusOK,
+			Message: "Using embedded role templates (no custom overrides)",
+		}
+	}
+
 	if len(missingPrompts) > 0 {
 		return &CheckResult{
 			Name:    c.Name(),
-			Status:  StatusWarning,
-			Message: fmt.Sprintf("%d role prompt template(s) missing", len(missingPrompts)),
-			Details: missingPrompts,
-			FixHint: "Run 'gt doctor --fix' to copy embedded templates to rig repos",
+			Status:  StatusOK,
+			Message: fmt.Sprintf("%d rig(s) using embedded templates for some roles", len(c.missingByRig)),
 		}
 	}
 

internal/git/git.go

@@ -116,13 +116,35 @@ func (g *Git) wrapError(err error, stdout, stderr string, args []string) error {
 
 // Clone clones a repository to the destination.
 func (g *Git) Clone(url, dest string) error {
-	cmd := exec.Command("git", "clone", url, dest)
+	// Ensure destination directory's parent exists
+	destParent := filepath.Dir(dest)
+	if err := os.MkdirAll(destParent, 0755); err != nil {
+		return fmt.Errorf("creating destination parent: %w", err)
+	}
+	// Run clone from a temporary directory to completely isolate from any
+	// git repo at the process cwd. Then move the result to the destination.
+	tmpDir, err := os.MkdirTemp("", "gt-clone-*")
+	if err != nil {
+		return fmt.Errorf("creating temp dir: %w", err)
+	}
+	defer func() { _ = os.RemoveAll(tmpDir) }()
+
+	tmpDest := filepath.Join(tmpDir, filepath.Base(dest))
+	cmd := exec.Command("git", "clone", url, tmpDest)
+	cmd.Dir = tmpDir
+	cmd.Env = append(os.Environ(), "GIT_CEILING_DIRECTORIES="+tmpDir)
 	var stdout, stderr bytes.Buffer
 	cmd.Stdout = &stdout
 	cmd.Stderr = &stderr
 	if err := cmd.Run(); err != nil {
 		return g.wrapError(err, stdout.String(), stderr.String(), []string{"clone", url})
 	}
+
+	// Move to final destination
+	if err := os.Rename(tmpDest, dest); err != nil {
+		return fmt.Errorf("moving clone to destination: %w", err)
+	}
+
 	// Configure hooks path for Gas Town clones
 	if err := configureHooksPath(dest); err != nil {
 		return err
@@ -134,13 +156,35 @@ func (g *Git) Clone(url, dest string) error {
 // CloneWithReference clones a repository using a local repo as an object reference.
 // This saves disk by sharing objects without changing remotes.
 func (g *Git) CloneWithReference(url, dest, reference string) error {
-	cmd := exec.Command("git", "clone", "--reference-if-able", reference, url, dest)
+	// Ensure destination directory's parent exists
+	destParent := filepath.Dir(dest)
+	if err := os.MkdirAll(destParent, 0755); err != nil {
+		return fmt.Errorf("creating destination parent: %w", err)
+	}
+	// Run clone from a temporary directory to completely isolate from any
+	// git repo at the process cwd. Then move the result to the destination.
+	tmpDir, err := os.MkdirTemp("", "gt-clone-*")
+	if err != nil {
+		return fmt.Errorf("creating temp dir: %w", err)
+	}
+	defer func() { _ = os.RemoveAll(tmpDir) }()
+
+	tmpDest := filepath.Join(tmpDir, filepath.Base(dest))
+	cmd := exec.Command("git", "clone", "--reference-if-able", reference, url, tmpDest)
+	cmd.Dir = tmpDir
+	cmd.Env = append(os.Environ(), "GIT_CEILING_DIRECTORIES="+tmpDir)
 	var stdout, stderr bytes.Buffer
 	cmd.Stdout = &stdout
 	cmd.Stderr = &stderr
 	if err := cmd.Run(); err != nil {
 		return g.wrapError(err, stdout.String(), stderr.String(), []string{"clone", "--reference-if-able", url})
 	}
+
+	// Move to final destination
+	if err := os.Rename(tmpDest, dest); err != nil {
+		return fmt.Errorf("moving clone to destination: %w", err)
+	}
+
 	// Configure hooks path for Gas Town clones
 	if err := configureHooksPath(dest); err != nil {
 		return err
@@ -152,13 +196,35 @@ func (g *Git) CloneWithReference(url, dest, reference string) error {
 // CloneBare clones a repository as a bare repo (no working directory).
 // This is used for the shared repo architecture where all worktrees share a single git database.
 func (g *Git) CloneBare(url, dest string) error {
-	cmd := exec.Command("git", "clone", "--bare", url, dest)
+	// Ensure destination directory's parent exists
+	destParent := filepath.Dir(dest)
+	if err := os.MkdirAll(destParent, 0755); err != nil {
+		return fmt.Errorf("creating destination parent: %w", err)
+	}
+	// Run clone from a temporary directory to completely isolate from any
+	// git repo at the process cwd. Then move the result to the destination.
+	tmpDir, err := os.MkdirTemp("", "gt-clone-*")
+	if err != nil {
+		return fmt.Errorf("creating temp dir: %w", err)
+	}
+	defer func() { _ = os.RemoveAll(tmpDir) }()
+
+	tmpDest := filepath.Join(tmpDir, filepath.Base(dest))
+	cmd := exec.Command("git", "clone", "--bare", url, tmpDest)
+	cmd.Dir = tmpDir
+	cmd.Env = append(os.Environ(), "GIT_CEILING_DIRECTORIES="+tmpDir)
 	var stdout, stderr bytes.Buffer
 	cmd.Stdout = &stdout
 	cmd.Stderr = &stderr
 	if err := cmd.Run(); err != nil {
 		return g.wrapError(err, stdout.String(), stderr.String(), []string{"clone", "--bare", url})
 	}
+
+	// Move to final destination
+	if err := os.Rename(tmpDest, dest); err != nil {
+		return fmt.Errorf("moving clone to destination: %w", err)
+	}
+
 	// Configure refspec so worktrees can fetch and see origin/* refs
 	return configureRefspec(dest)
 }
@@ -212,13 +278,35 @@ func configureRefspec(repoPath string) error {
 
 // CloneBareWithReference clones a bare repository using a local repo as an object reference.
 func (g *Git) CloneBareWithReference(url, dest, reference string) error {
-	cmd := exec.Command("git", "clone", "--bare", "--reference-if-able", reference, url, dest)
+	// Ensure destination directory's parent exists
+	destParent := filepath.Dir(dest)
+	if err := os.MkdirAll(destParent, 0755); err != nil {
+		return fmt.Errorf("creating destination parent: %w", err)
+	}
+	// Run clone from a temporary directory to completely isolate from any
+	// git repo at the process cwd. Then move the result to the destination.
+	tmpDir, err := os.MkdirTemp("", "gt-clone-*")
+	if err != nil {
+		return fmt.Errorf("creating temp dir: %w", err)
+	}
+	defer func() { _ = os.RemoveAll(tmpDir) }()
+
+	tmpDest := filepath.Join(tmpDir, filepath.Base(dest))
+	cmd := exec.Command("git", "clone", "--bare", "--reference-if-able", reference, url, tmpDest)
+	cmd.Dir = tmpDir
+	cmd.Env = append(os.Environ(), "GIT_CEILING_DIRECTORIES="+tmpDir)
 	var stdout, stderr bytes.Buffer
 	cmd.Stdout = &stdout
 	cmd.Stderr = &stderr
 	if err := cmd.Run(); err != nil {
 		return g.wrapError(err, stdout.String(), stderr.String(), []string{"clone", "--bare", "--reference-if-able", url})
 	}
+
+	// Move to final destination
+	if err := os.Rename(tmpDest, dest); err != nil {
+		return fmt.Errorf("moving clone to destination: %w", err)
+	}
+
 	// Configure refspec so worktrees can fetch and see origin/* refs
 	return configureRefspec(dest)
 }