diff --git a/cmd/gc/bd_env.go b/cmd/gc/bd_env.go
index 681ab244eb..8e8c14954b 100644
--- a/cmd/gc/bd_env.go
+++ b/cmd/gc/bd_env.go
@@ -37,6 +37,7 @@ func bdStoreForCity(dir, cityPath string) *beads.BdStore {
 	if err != nil {
 		cfg = nil
 	}
+	reapStaleBdExportJSONL(dir)
 	return beads.NewBdStoreWithPrefix(dir, bdCommandRunnerForCity(cityPath), issuePrefixForScope(dir, cityPath, cfg))
 }
 
@@ -53,9 +54,84 @@ func bdStoreForRig(rigDir, cityPath string, cfg *config.City, knownPrefix ...str
 			}
 		}
 	}
+	reapStaleBdExportJSONL(rigDir)
 	return beads.NewBdStoreWithPrefix(rigDir, bdCommandRunnerForRig(cityPath, cfg, rigDir), prefix)
 }
 
+// reapStaleBdExportJSONL removes .beads/issues.jsonl best-effort when the
+// scope is gc-managed. The file is a stale export from when bd's auto-export
+// was on (the upstream default); keeping it on disk causes bd 1.x to detect
+// a "fresh clone" / "empty database" on the next write and stall bd create /
+// gc mail send for the full 2m subprocess timeout while it re-imports the
+// JSONL (sa-41j3kp).
+//
+// Cleanup conditions (any of which proves the scope is gc-managed and the
+// JSONL is therefore stale):
+//
+//   - config.yaml explicitly sets export.auto:false (PR 1965 canonical state)
+//   - config.yaml's gc.endpoint_origin is one of the managed origins
+//
+// Best-effort: any error is ignored because the env-var BD_EXPORT_AUTO=false
+// in bdRuntimeEnv is a second line of defense, and a concurrent reader of the
+// file (e.g., a bd-aware viewer) shouldn't fail the caller's operation. Reads
+// use os.Stat/os.Remove (not fsys.OSFS) so the helper stays callable from
+// store constructors that don't carry an fs seam.
+func reapStaleBdExportJSONL(scopeRoot string) {
+	scopeRoot = strings.TrimSpace(scopeRoot)
+	if scopeRoot == "" {
+		return
+	}
+	jsonlPath := filepath.Join(scopeRoot, ".beads", "issues.jsonl")
+	if _, err := os.Stat(jsonlPath); err != nil {
+		// Fast path: no file → nothing to do. This is the steady state
+		// once the cleanup has run once, so the rest of the helper is
+		// only reached during the one-shot transition.
+		return
+	}
+	if !scopeIsGCManaged(scopeRoot) {
+		// Unmanaged scope: leave the file alone. Removing it under those
+		// conditions could race with a legitimate auto-exporter (e.g., a
+		// rig that opted out of managed canonicalization).
+		return
+	}
+	_ = os.Remove(jsonlPath)
+}
+
+// scopeIsGCManaged reports whether a scope's .beads/config.yaml proves the
+// scope is gc-managed under the canonical (non-explicit) shape. Either of
+// two signals counts as proof:
+//   - export.auto is explicitly false (PR 1965 wrote it; the user did not
+//     opt back into auto-export afterward)
+//   - gc.endpoint_origin is one of the canonical managed origins (the scope
+//     was initialized by gc, even if the export.auto key has not yet been
+//     normalized into the config on disk)
+//
+// Either signal alone is sufficient: the first covers post-normalization
+// state, the second covers the transitional state where samtown-style
+// long-lived cities still have a pre-PR-1965 config but were always
+// gc-managed.
+//
+// EndpointOriginExplicit is intentionally excluded: per PR 1965, that is
+// the deliberate opt-out path for rigs that want to keep JSONL-based
+// sharing, so issues.jsonl there is load-bearing, not stale.
+func scopeIsGCManaged(scopeRoot string) bool {
+	configPath := filepath.Join(scopeRoot, ".beads", "config.yaml")
+	if autoExport, ok, err := contract.ReadExportAuto(fsys.OSFS{}, configPath); err == nil && ok && !autoExport {
+		return true
+	}
+	state, ok, err := contract.ReadConfigState(fsys.OSFS{}, configPath)
+	if err != nil || !ok {
+		return false
+	}
+	switch state.EndpointOrigin {
+	case contract.EndpointOriginManagedCity,
+		contract.EndpointOriginCityCanonical,
+		contract.EndpointOriginInheritedCity:
+		return true
+	}
+	return false
+}
+
 func controlBdStoreForCity(dir, cityPath string, cfg *config.City) *beads.BdStore {
 	return beads.NewBdStoreWithPrefix(dir, controlBdCommandRunnerForCity(cityPath), issuePrefixForScope(dir, cityPath, cfg))
 }
@@ -548,6 +624,16 @@ func bdRuntimeEnv(cityPath string) map[string]string {
 	// dolt.auto-start:false config (beads resolveAutoStart priority bug) and
 	// starts rogue servers from the agent's cwd with the wrong data_dir.
 	env["BEADS_DOLT_AUTO_START"] = "0"
+	// Suppress bd's auto-export of issues.jsonl on every write. The canonical
+	// config also persists export.auto:false (see internal/beads/contract/files.go),
+	// but the env var is the bulletproof per-invocation guard: it covers fresh
+	// scopes whose config has not yet been canonicalized, and it short-circuits
+	// the export → next-write-auto-import stall cycle (sa-41j3kp) even when an
+	// out-of-band caller has left a stale .beads/issues.jsonl on disk. Without
+	// this, bd's "auto-importing N bytes ... into empty database" path can
+	// stall bd create / gc mail send for the full 2m subprocess timeout on
+	// large datasets.
+	env["BD_EXPORT_AUTO"] = "false"
 	if !cityUsesBdStoreContract(cityPath) {
 		return env
 	}
diff --git a/cmd/gc/bd_env_test.go b/cmd/gc/bd_env_test.go
index ba4286568e..1076651ecf 100644
--- a/cmd/gc/bd_env_test.go
+++ b/cmd/gc/bd_env_test.go
@@ -3064,3 +3064,158 @@ func TestControlBdCommandRunnerDefaultsBeadsActorToControllerWhenUnset(t *testin
 		t.Fatalf("BD_EXPORT_AUTO = %q, want false", got)
 	}
 }
+
+// TestBdRuntimeEnvDisablesAutoExport pins the env-var defense against
+// bd's auto-export-on-write trap (sa-41j3kp): every gc-initiated bd call
+// must set BD_EXPORT_AUTO=false so that even if .beads/config.yaml has not
+// yet been canonicalized with export.auto:false (older cities pre-PR-1965,
+// fresh inits, rigs that have not reached normalization), bd's auto-export
+// of issues.jsonl on every write is suppressed. Without this, the next bd
+// write re-creates the 15MB JSONL, and the bd write after that stalls for
+// the full 2m subprocess timeout while bd re-imports the file.
+func TestBdRuntimeEnvDisablesAutoExport(t *testing.T) {
+	t.Setenv("GC_BEADS", "bd")
+	t.Setenv("GC_DOLT", "skip")
+
+	cityPath := t.TempDir()
+	env := bdRuntimeEnv(cityPath)
+
+	if got := env["BD_EXPORT_AUTO"]; got != "false" {
+		t.Fatalf("BD_EXPORT_AUTO = %q, want false (auto-export-on-write suppression for sa-41j3kp)", got)
+	}
+}
+
+// TestScopeIsGCManagedRecognizesExplicitAutoOff verifies that a config with
+// export.auto:false is recognized as gc-managed even when gc.endpoint_origin
+// is absent. This is the steady-state signal post-PR-1965.
+func TestScopeIsGCManagedRecognizesExplicitAutoOff(t *testing.T) {
+	scope := t.TempDir()
+	beadsDir := filepath.Join(scope, ".beads")
+	if err := os.MkdirAll(beadsDir, 0o755); err != nil {
+		t.Fatalf("mkdir: %v", err)
+	}
+	if err := os.WriteFile(filepath.Join(beadsDir, "config.yaml"),
+		[]byte("issue_prefix: zz\nexport.auto: false\n"), 0o644); err != nil {
+		t.Fatalf("write config: %v", err)
+	}
+
+	if !scopeIsGCManaged(scope) {
+		t.Fatalf("scopeIsGCManaged = false, want true for explicit export.auto:false")
+	}
+}
+
+// TestScopeIsGCManagedRecognizesManagedOrigin verifies that a long-lived
+// city whose config still pre-dates PR 1965 (export.auto absent) is still
+// recognized as gc-managed because gc.endpoint_origin proves it. This is
+// the transitional signal — without it the jsonl reaper would refuse to
+// clean up samtown-style cities until they hit a canonicalization event.
+func TestScopeIsGCManagedRecognizesManagedOrigin(t *testing.T) {
+	scope := t.TempDir()
+	beadsDir := filepath.Join(scope, ".beads")
+	if err := os.MkdirAll(beadsDir, 0o755); err != nil {
+		t.Fatalf("mkdir: %v", err)
+	}
+	if err := os.WriteFile(filepath.Join(beadsDir, "config.yaml"),
+		[]byte("issue_prefix: zz\ngc.endpoint_origin: managed_city\n"), 0o644); err != nil {
+		t.Fatalf("write config: %v", err)
+	}
+
+	if !scopeIsGCManaged(scope) {
+		t.Fatalf("scopeIsGCManaged = false, want true for gc.endpoint_origin: managed_city")
+	}
+}
+
+// TestScopeIsGCManagedDoesNotClaimExplicitOptOut verifies the carve-out
+// for rigs that deliberately keep JSONL-based sharing. Per PR 1965 docs,
+// gc.endpoint_origin: explicit is the supported opt-out path; issues.jsonl
+// there is load-bearing, not stale, so scopeIsGCManaged must return false.
+func TestScopeIsGCManagedDoesNotClaimExplicitOptOut(t *testing.T) {
+	scope := t.TempDir()
+	beadsDir := filepath.Join(scope, ".beads")
+	if err := os.MkdirAll(beadsDir, 0o755); err != nil {
+		t.Fatalf("mkdir: %v", err)
+	}
+	if err := os.WriteFile(filepath.Join(beadsDir, "config.yaml"),
+		[]byte("issue_prefix: zz\ngc.endpoint_origin: explicit\n"), 0o644); err != nil {
+		t.Fatalf("write config: %v", err)
+	}
+
+	if scopeIsGCManaged(scope) {
+		t.Fatalf("scopeIsGCManaged = true, want false for explicit opt-out")
+	}
+}
+
+// TestReapStaleBdExportJSONLRemovesFileOnManagedScope verifies the
+// transitional cleanup that breaks the sa-41j3kp loop on samtown-style
+// long-lived cities. issues.jsonl from a pre-PR-1965 auto-export is
+// removed on the next bd-store construction, so the next bd create does
+// not stall on auto-import.
+func TestReapStaleBdExportJSONLRemovesFileOnManagedScope(t *testing.T) {
+	scope := t.TempDir()
+	beadsDir := filepath.Join(scope, ".beads")
+	if err := os.MkdirAll(beadsDir, 0o755); err != nil {
+		t.Fatalf("mkdir: %v", err)
+	}
+	jsonlPath := filepath.Join(beadsDir, "issues.jsonl")
+	if err := os.WriteFile(jsonlPath, []byte(`{"_type":"issue","id":"zz-1"}`+"\n"), 0o644); err != nil {
+		t.Fatalf("write jsonl: %v", err)
+	}
+	if err := os.WriteFile(filepath.Join(beadsDir, "config.yaml"),
+		[]byte("issue_prefix: zz\ngc.endpoint_origin: managed_city\n"), 0o644); err != nil {
+		t.Fatalf("write config: %v", err)
+	}
+
+	reapStaleBdExportJSONL(scope)
+
+	if _, err := os.Stat(jsonlPath); !os.IsNotExist(err) {
+		t.Fatalf("jsonl present after reap; stat err = %v, want IsNotExist", err)
+	}
+}
+
+// TestReapStaleBdExportJSONLLeavesFileOnExplicitOptOut verifies the
+// opt-out path: rigs with gc.endpoint_origin: explicit keep issues.jsonl
+// because they're deliberately using JSONL-based sharing.
+func TestReapStaleBdExportJSONLLeavesFileOnExplicitOptOut(t *testing.T) {
+	scope := t.TempDir()
+	beadsDir := filepath.Join(scope, ".beads")
+	if err := os.MkdirAll(beadsDir, 0o755); err != nil {
+		t.Fatalf("mkdir: %v", err)
+	}
+	jsonlPath := filepath.Join(beadsDir, "issues.jsonl")
+	if err := os.WriteFile(jsonlPath, []byte(`{"_type":"issue","id":"zz-1"}`+"\n"), 0o644); err != nil {
+		t.Fatalf("write jsonl: %v", err)
+	}
+	if err := os.WriteFile(filepath.Join(beadsDir, "config.yaml"),
+		[]byte("issue_prefix: zz\ngc.endpoint_origin: explicit\n"), 0o644); err != nil {
+		t.Fatalf("write config: %v", err)
+	}
+
+	reapStaleBdExportJSONL(scope)
+
+	if _, err := os.Stat(jsonlPath); err != nil {
+		t.Fatalf("jsonl removed on explicit opt-out; stat err = %v, want nil", err)
+	}
+}
+
+// TestReapStaleBdExportJSONLLeavesFileOnUnmanagedScope verifies that an
+// unmanaged scope (no config.yaml, or config without any gc/managed signal)
+// keeps issues.jsonl intact. The reaper must not be aggressive on scopes
+// that gc does not own.
+func TestReapStaleBdExportJSONLLeavesFileOnUnmanagedScope(t *testing.T) {
+	scope := t.TempDir()
+	beadsDir := filepath.Join(scope, ".beads")
+	if err := os.MkdirAll(beadsDir, 0o755); err != nil {
+		t.Fatalf("mkdir: %v", err)
+	}
+	jsonlPath := filepath.Join(beadsDir, "issues.jsonl")
+	if err := os.WriteFile(jsonlPath, []byte(`{"_type":"issue","id":"zz-1"}`+"\n"), 0o644); err != nil {
+		t.Fatalf("write jsonl: %v", err)
+	}
+	// No config.yaml at all — definitely not gc-managed.
+
+	reapStaleBdExportJSONL(scope)
+
+	if _, err := os.Stat(jsonlPath); err != nil {
+		t.Fatalf("jsonl removed on unmanaged scope; stat err = %v, want nil", err)
+	}
+}
diff --git a/cmd/gc/beads_provider_lifecycle.go b/cmd/gc/beads_provider_lifecycle.go
index 519c9fe068..13db5fadfa 100644
--- a/cmd/gc/beads_provider_lifecycle.go
+++ b/cmd/gc/beads_provider_lifecycle.go
@@ -325,8 +325,36 @@ func ensureCanonicalScopeConfigState(fs fsys.FS, dir string, state contract.Conf
 	if err := ensureBeadsDir(fs, beadsDir); err != nil {
 		return err
 	}
-	_, err := contract.EnsureCanonicalConfig(fs, filepath.Join(beadsDir, "config.yaml"), state)
-	return err
+	changed, err := contract.EnsureCanonicalConfig(fs, filepath.Join(beadsDir, "config.yaml"), state)
+	if err != nil {
+		return err
+	}
+	if changed {
+		// PR 1965 made export.auto:false canonical, but a pre-existing
+		// .beads/issues.jsonl from before this normalization still triggers
+		// bd's auto-import-on-write trap (sa-41j3kp) — bd sees the file,
+		// detects a "stale DB", and stalls bd create for the full 2m
+		// subprocess timeout while it re-imports the JSONL. The file is a
+		// stale export from when auto-export was on; with the canonical
+		// config now suppressing auto-export, nothing will refresh it, so
+		// keeping it on disk is pure liability. Remove best-effort.
+		removeStaleBdExportJSONL(fs, beadsDir)
+	}
+	return nil
+}
+
+// removeStaleBdExportJSONL removes .beads/issues.jsonl if present. Called after
+// EnsureCanonicalConfig writes export.auto:false, since the file is a stale
+// export that bd's auto-import path would otherwise re-load on every write,
+// stalling bd create for the full subprocess timeout on large datasets.
+// Best-effort: any error is non-fatal because the env-var BD_EXPORT_AUTO=false
+// path (bdRuntimeEnv) is a second line of defense for gc-initiated calls.
+func removeStaleBdExportJSONL(fs fsys.FS, beadsDir string) {
+	path := filepath.Join(beadsDir, "issues.jsonl")
+	if _, err := fs.Stat(path); err != nil {
+		return
+	}
+	_ = fs.Remove(path)
 }
 
 func seedDeferredManagedBeads(cityPath, dir, prefix, doltDatabase string) {
diff --git a/internal/beads/contract/files.go b/internal/beads/contract/files.go
index 4bd1efc780..329f1f75ca 100644
--- a/internal/beads/contract/files.go
+++ b/internal/beads/contract/files.go
@@ -118,6 +118,30 @@ func ReadAutoStartDisabled(fs fsys.FS, path string) (bool, error) {
 	return false, nil
 }
 
+// ReadExportAuto returns the configured value of export.auto along with a
+// presence indicator. ok=false means the key is absent from the config (the
+// upstream bd default is true). Used by gc to gate cleanup of stale
+// .beads/issues.jsonl exports: when export.auto is explicitly false, the
+// JSONL is a stale artifact that bd's auto-import-on-write path (sa-41j3kp)
+// would otherwise reload on every write, stalling bd create for minutes on
+// large datasets.
+func ReadExportAuto(fs fsys.FS, path string) (value bool, ok bool, err error) {
+	doc, err := readConfigDoc(fs, path)
+	if err != nil {
+		if os.IsNotExist(err) {
+			return false, false, nil
+		}
+		if raw, scanOK := scanConfigLineValue(fs, path, "export.auto:"); scanOK {
+			return raw == "true", true, nil
+		}
+		return false, false, err
+	}
+	if raw, present := configStringValue(mappingRoot(doc), "export.auto"); present {
+		return raw == "true", true, nil
+	}
+	return false, false, nil
+}
+
 // ReadEndpointStatus reads gc.endpoint_status when present.
 func ReadEndpointStatus(fs fsys.FS, path string) (EndpointStatus, bool, error) {
 	doc, err := readConfigDoc(fs, path)
diff --git a/internal/beads/contract/files_test.go b/internal/beads/contract/files_test.go
index 6df3fe4a36..4b751ef1cd 100644
--- a/internal/beads/contract/files_test.go
+++ b/internal/beads/contract/files_test.go
@@ -571,6 +571,73 @@ func TestReadAutoStartDisabledFallsBackToLineScanOnMalformedYAML(t *testing.T) {
 	}
 }
 
+func TestReadExportAuto(t *testing.T) {
+	tests := []struct {
+		name      string
+		yaml      string
+		wantValue bool
+		wantOK    bool
+	}{
+		{
+			name:      "explicit false",
+			yaml:      "issue_prefix: zz\nexport.auto: false\n",
+			wantValue: false,
+			wantOK:    true,
+		},
+		{
+			name:      "explicit true",
+			yaml:      "issue_prefix: zz\nexport.auto: true\n",
+			wantValue: true,
+			wantOK:    true,
+		},
+		{
+			name:      "absent",
+			yaml:      "issue_prefix: zz\n",
+			wantValue: false,
+			wantOK:    false,
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			fs := fsys.OSFS{}
+			dir := t.TempDir()
+			path := filepath.Join(dir, "config.yaml")
+			if err := fs.WriteFile(path, []byte(tt.yaml), 0o644); err != nil {
+				t.Fatal(err)
+			}
+
+			gotValue, gotOK, err := ReadExportAuto(fs, path)
+			if err != nil {
+				t.Fatalf("ReadExportAuto() error = %v", err)
+			}
+			if gotOK != tt.wantOK {
+				t.Errorf("ReadExportAuto() ok = %v, want %v", gotOK, tt.wantOK)
+			}
+			if gotValue != tt.wantValue {
+				t.Errorf("ReadExportAuto() value = %v, want %v", gotValue, tt.wantValue)
+			}
+		})
+	}
+}
+
+func TestReadExportAutoOnMissingFileReturnsAbsent(t *testing.T) {
+	fs := fsys.OSFS{}
+	dir := t.TempDir()
+	path := filepath.Join(dir, "missing.yaml")
+
+	gotValue, gotOK, err := ReadExportAuto(fs, path)
+	if err != nil {
+		t.Fatalf("ReadExportAuto() error = %v, want nil for missing file", err)
+	}
+	if gotOK {
+		t.Errorf("ReadExportAuto() ok = true, want false for missing file")
+	}
+	if gotValue {
+		t.Errorf("ReadExportAuto() value = true, want false for missing file")
+	}
+}
+
 func TestEnsureCanonicalMetadataPreservesUnknownKeysAndScrubsDeprecatedOnes(t *testing.T) {
 	fs := fsys.OSFS{}
 	dir := t.TempDir()