Fix configure flag precedence and add provider fallback logging

- Process both --checkpoint-remote and --summarize-provider flags when
  set together instead of silently dropping summary provider flags
- Log when falling back to Claude Code (no providers installed, or
  non-interactive mode with multiple providers)
- Make persistSummaryProviderSelection failure non-fatal: log warning
  and continue with resolved provider instead of aborting

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Entire-Checkpoint: 6aa3fd749d78

Author: peyton-alt

cmd/entire/cli/explain_summary_provider.go

@@ -8,6 +8,7 @@ import (
 
 	"github.com/entireio/cli/cmd/entire/cli/agent"
 	"github.com/entireio/cli/cmd/entire/cli/agent/types"
+	"github.com/entireio/cli/cmd/entire/cli/logging"
 	"github.com/entireio/cli/cmd/entire/cli/paths"
 	"github.com/entireio/cli/cmd/entire/cli/settings"
 	"github.com/entireio/cli/cmd/entire/cli/summarize"
@@ -49,18 +50,21 @@ func resolveCheckpointSummaryProvider(ctx context.Context, w io.Writer) (*checkp
 
 	switch len(candidates) {
 	case 0:
+		logging.Info(ctx, "no summary-capable agents installed, falling back to Claude Code")
 		return buildCheckpointSummaryProvider(agent.AgentNameClaudeCode, "")
 	case 1:
 		provider, err := buildCheckpointSummaryProvider(candidates[0].Name, "")
 		if err != nil {
 			return nil, err
 		}
 		if saveErr := persistSummaryProviderSelection(ctx, provider.Name, provider.Model); saveErr != nil {
-			return nil, saveErr
+			logging.Warn(ctx, "failed to save summary provider selection, continuing without persistence",
+				"error", saveErr.Error())
 		}
 		return provider, nil
 	default:
 		if !canPromptInteractively() {
+			logging.Info(ctx, "non-interactive mode with multiple summary providers, falling back to Claude Code")
 			return buildCheckpointSummaryProvider(agent.AgentNameClaudeCode, "")
 		}
 
@@ -74,7 +78,8 @@ func resolveCheckpointSummaryProvider(ctx context.Context, w io.Writer) (*checkp
 			return nil, err
 		}
 		if saveErr := persistSummaryProviderSelection(ctx, provider.Name, provider.Model); saveErr != nil {
-			return nil, saveErr
+			logging.Warn(ctx, "failed to save summary provider selection, continuing without persistence",
+				"error", saveErr.Error())
 		}
 		fmt.Fprintf(w, "Using %s for summary generation.\n", provider.DisplayName)
 		return provider, nil

cmd/entire/cli/setup.go

@@ -510,12 +510,19 @@ Use --remove to remove a specific agent non-interactively:
 				return setupAgentHooksNonInteractive(ctx, cmd.OutOrStdout(), ag, opts)
 			}
 
-			// Settings-only mode: update strategy options without agent selection
-			if hasStrategyFlags(cmd) && settings.IsSetUpAny(ctx) {
-				return updateStrategyOptions(ctx, cmd.OutOrStdout(), opts)
-			}
-			if hasSummaryProviderFlags(cmd) && settings.IsSetUpAny(ctx) {
-				return updateSummaryGenerationSettings(ctx, cmd.OutOrStdout(), summarizeProvider, summarizeModel, opts)
+			// Settings-only mode: update strategy options / summary provider without agent selection
+			if settings.IsSetUpAny(ctx) && (hasStrategyFlags(cmd) || hasSummaryProviderFlags(cmd)) {
+				if hasStrategyFlags(cmd) {
+					if err := updateStrategyOptions(ctx, cmd.OutOrStdout(), opts); err != nil {
+						return err
+					}
+				}
+				if hasSummaryProviderFlags(cmd) {
+					if err := updateSummaryGenerationSettings(ctx, cmd.OutOrStdout(), summarizeProvider, summarizeModel, opts); err != nil {
+						return err
+					}
+				}
+				return nil
 			}
 
 			// If already set up, show agents and let user add more