diff --git a/core/cli/deadline_test.go b/core/cli/deadline_test.go
new file mode 100644
index 0000000..8bc8008
--- /dev/null
+++ b/core/cli/deadline_test.go
@@ -0,0 +1,90 @@
+package cli
+
+import (
+	"context"
+	"strings"
+	"testing"
+	"time"
+
+	"github.com/spf13/cobra"
+
+	"github.com/NDDev-OpenNetwork/github-device-sync/core/domain"
+)
+
+// A deadline is not a changed repository. `module update-pin --apply` used to
+// report GDS_STALE_PLAN when its own context expired mid-observation, which
+// sends the reader looking for a concurrent writer that does not exist.
+func TestExpiredDeadlineIsNamedAsADeadline(t *testing.T) {
+	exitCode, envelope, _ := executeJSON(t, "--json", "--timeout", "1ns", "doctor")
+	if exitCode == 0 {
+		t.Fatalf("an expired deadline must not succeed: %#v", envelope)
+	}
+	if !containsFinding(envelope.Findings, "GDS_COMMAND_DEADLINE_EXCEEDED") {
+		t.Fatalf("expired deadline was not named as one: %#v", envelope.Findings)
+	}
+	for _, finding := range envelope.Findings {
+		if finding.Code != "GDS_COMMAND_DEADLINE_EXCEEDED" {
+			continue
+		}
+		if !strings.Contains(finding.Message, "not a changed repository") {
+			t.Fatalf("deadline finding does not say what it is not: %q", finding.Message)
+		}
+		if finding.Evidence["flag"] != "--timeout" {
+			t.Fatalf("deadline finding does not name the flag: %#v", finding.Evidence)
+		}
+	}
+}
+
+// A successful command must not collect the finding just because it finished
+// near its deadline.
+func TestSuccessfulCommandIsNotLabelledADeadline(t *testing.T) {
+	_, envelope, _ := executeJSON(t, "--json", "identity", "new", "device")
+	if containsFinding(envelope.Findings, "GDS_COMMAND_DEADLINE_EXCEEDED") {
+		t.Fatalf("a successful command must not report a deadline: %#v", envelope.Findings)
+	}
+}
+
+func deadlineFor(t *testing.T, lanes bool, flagSet bool) time.Duration {
+	t.Helper()
+	runner := &executor{options: options{cwd: ".", timeout: 2 * time.Minute}}
+	command := &cobra.Command{Use: "probe"}
+	command.Flags().DurationVar(&runner.options.timeout, "timeout", 2*time.Minute, "command deadline")
+	if flagSet {
+		if err := command.Flags().Set("timeout", "90s"); err != nil {
+			t.Fatal(err)
+		}
+	}
+	command.SetContext(context.Background())
+	var observed time.Duration
+	operation := func(ctx context.Context) domain.Envelope {
+		if deadline, ok := ctx.Deadline(); ok {
+			observed = time.Until(deadline).Round(time.Second)
+		}
+		return domain.Success("probe", nil)
+	}
+	var err error
+	if lanes {
+		err = runner.runLanes(command, operation)
+	} else {
+		err = runner.run(command, operation)
+	}
+	if err != nil {
+		t.Fatal(err)
+	}
+	return observed
+}
+
+// Commands that execute another repository's verification lanes need more than
+// the deadline sized for a read -- update-pin runs them twice, once to plan and
+// once to re-observe before mutating -- but an explicit --timeout always wins.
+func TestLaneCommandsGetALongerDefaultUnlessTheCallerChose(t *testing.T) {
+	if got := deadlineFor(t, false, false); got > 3*time.Minute {
+		t.Fatalf("ordinary command deadline = %s, want the 2m read default", got)
+	}
+	if got := deadlineFor(t, true, false); got < 15*time.Minute {
+		t.Fatalf("lane command deadline = %s, want the longer default", got)
+	}
+	if got := deadlineFor(t, true, true); got > 2*time.Minute {
+		t.Fatalf("explicit --timeout was overridden: %s", got)
+	}
+}
diff --git a/core/cli/root.go b/core/cli/root.go
index daccfc0..95261c8 100644
--- a/core/cli/root.go
+++ b/core/cli/root.go
@@ -4,6 +4,7 @@ package cli
 import (
 	"context"
 	"encoding/json"
+	"errors"
 	"fmt"
 	"io"
 	"runtime"
@@ -1859,7 +1860,9 @@ func (executor *executor) modulePinCommand() *cobra.Command {
 		Use: "update-pin", Short: "Update one exact consumer gitlink to a finalized module commit",
 		Args: cobra.NoArgs,
 		RunE: func(child *cobra.Command, _ []string) error {
-			return executor.run(child, func(ctx context.Context) domain.Envelope {
+			// Plan and apply both run the module's required lanes at the target
+			// commit, so this needs the lane deadline rather than the read one.
+			return executor.runLanes(child, func(ctx context.Context) domain.Envelope {
 				if selectedModes(plan, applyPlanID, verifyOperationID) != 1 {
 					return domain.NewEnvelope("gds module update-pin", domain.ExitInput, nil, domain.Finding{
 						Code: "GDS_MODULE_PIN_MODE_REQUIRED", Severity: domain.SeverityHigh,
@@ -2753,9 +2756,34 @@ func (executor *executor) doctorCommand() *cobra.Command {
 	return command
 }
 
+// laneCommandTimeout is the default deadline for commands that execute another
+// repository's declared verification lanes rather than reading state. Two
+// minutes is right for a read and far too short for a command that runs a
+// module's test suite twice -- once to plan, once to re-observe before the
+// mutation -- which is how a working `module update-pin` came to look broken.
+const laneCommandTimeout = 20 * time.Minute
+
 func (executor *executor) run(
 	command *cobra.Command,
 	operation func(context.Context) domain.Envelope,
+) error {
+	return executor.runWithin(command, 0, operation)
+}
+
+// runLanes is run for commands that execute a module's verification lanes. An
+// explicit --timeout always wins; the longer default applies only when the
+// caller did not choose one.
+func (executor *executor) runLanes(
+	command *cobra.Command,
+	operation func(context.Context) domain.Envelope,
+) error {
+	return executor.runWithin(command, laneCommandTimeout, operation)
+}
+
+func (executor *executor) runWithin(
+	command *cobra.Command,
+	minimum time.Duration,
+	operation func(context.Context) domain.Envelope,
 ) error {
 	if executor.options.timeout <= 0 {
 		envelope := domain.NewEnvelope("gds "+command.Name(), domain.ExitInput, nil, domain.Finding{
@@ -2766,9 +2794,26 @@ func (executor *executor) run(
 		executor.result = &envelope
 		return nil
 	}
-	ctx, cancel := context.WithTimeout(command.Context(), executor.options.timeout)
+	deadline := executor.options.timeout
+	if minimum > deadline && !command.Flags().Changed("timeout") {
+		deadline = minimum
+	}
+	ctx, cancel := context.WithTimeout(command.Context(), deadline)
 	defer cancel()
 	envelope := operation(ctx)
+	// A deadline is not a changed repository. Without this, an expired context
+	// surfaces as whatever the interrupted step reported -- for update-pin that
+	// was GDS_STALE_PLAN, "the repository changed before its first mutation
+	// step", which sends the reader looking for a concurrent writer that does
+	// not exist. Say what actually happened, and say how long it had.
+	if errors.Is(ctx.Err(), context.DeadlineExceeded) && envelope.ExitCode != 0 {
+		envelope.Findings = append(envelope.Findings, domain.Finding{
+			Code:     "GDS_COMMAND_DEADLINE_EXCEEDED",
+			Severity: domain.SeverityHigh,
+			Message:  "The command deadline expired before the operation finished; any earlier finding describes an interrupted step, not a changed repository.",
+			Evidence: map[string]any{"deadline": deadline.String(), "flag": "--timeout"},
+		})
+	}
 	executor.result = &envelope
 	return nil
 }
diff --git a/docs/contracts/lifecycles-v1.md b/docs/contracts/lifecycles-v1.md
index 45b48a9..99f81c3 100644
--- a/docs/contracts/lifecycles-v1.md
+++ b/docs/contracts/lifecycles-v1.md
@@ -139,6 +139,16 @@ absent one: the consumer holds the commit it is about to pin. The relaxation is
 exactly one gitlink wide; a staged, untracked or conflicted path, or a second
 unstaged one, still refuses with `GDS_MODULE_PIN_CONSUMER_STATE_UNSAFE`.
 
+`update-pin` runs the module's required lanes twice -- once when planning at
+the target commit, and once when the engine re-observes its preconditions before
+the mutation -- so it defaults to a twenty-minute deadline rather than the
+two-minute one sized for a read. An explicit `--timeout` always wins. Before
+that, the default expired mid-observation and the engine reported
+`GDS_STALE_PLAN`, "the repository changed before its first mutation step", which
+sends the reader looking for a concurrent writer that does not exist. Any
+command whose deadline expires now also carries
+`GDS_COMMAND_DEADLINE_EXCEEDED`, naming the deadline and the flag.
+
 Applying a pin needs no approval. The only mutation is a gitlink rewrite in the
 consumer's own working tree: it writes no provider, replaces no credential and
 publishes nothing, and the consumer's pull request and checks are its real gate.