Improve staleness check error handling and optimization (bd-n4td, bd-o4qy, bd-c4rq)

This commit implements three related improvements to database staleness checking:

**bd-n4td (P2): Add warning when staleness check errors**
- Added stderr warnings when CheckStaleness fails in ensureDatabaseFresh
- Users now see "Warning: could not check database staleness: <error>"
- Provides visibility into staleness check failures while allowing operations to proceed

**bd-o4qy (P2): Improve CheckStaleness error handling**
- Updated CheckStaleness to distinguish between expected and abnormal conditions:
  * Returns (false, nil) for expected "no data yet" scenarios (missing metadata, missing JSONL)
  * Returns (false, err) for abnormal errors (glob failures, permission errors)
- Updated RPC server (2 locations) to log staleness errors but allow requests to proceed
- Prevents blocking operations due to transient staleness check issues
- Added comprehensive function documentation

**bd-c4rq (P3): Refactor staleness check to avoid function call overhead**
- Moved daemon check from inside ensureDatabaseFresh to all 8 call sites
- Avoids unnecessary function call when running in daemon mode
- Updated: list.go, info.go, status.go, show.go, stale.go, duplicates.go, ready.go, validate.go
- Extracted staleness functions to new staleness.go for better organization

**Code review fixes:**
- Removed dead code in CheckStaleness (unreachable jsonlPath == "" check)
- Removed unused ensureDatabaseFreshQuiet function

**Files changed:**
- New: cmd/bd/staleness.go (extracted staleness checking functions)
- Modified: 8 command files (added daemon check before staleness calls)
- Modified: internal/autoimport/autoimport.go (improved error handling)
- Modified: internal/rpc/server_export_import_auto.go (handle errors gracefully)

cmd/bd/duplicates.go

@@ -33,6 +33,16 @@ Example:
 		dryRun, _ := cmd.Flags().GetBool("dry-run")
 		// Use global jsonOutput set by PersistentPreRun
 		ctx := context.Background()
+
+		// Check database freshness before reading (bd-2q6d, bd-c4rq)
+		// Skip check when using daemon (daemon auto-imports on staleness)
+		if daemonClient == nil {
+			if err := ensureDatabaseFresh(ctx); err != nil {
+				fmt.Fprintf(os.Stderr, "Error: %v\n", err)
+				os.Exit(1)
+			}
+		}
+
 		// Get all issues
 		allIssues, err := store.SearchIssues(ctx, "", types.IssueFilter{})
 		if err != nil {

cmd/bd/info.go

@@ -4,6 +4,7 @@ import (
 	"context"
 	"encoding/json"
 	"fmt"
+	"os"
 	"path/filepath"
 	"strings"
 
@@ -88,6 +89,16 @@ Examples:
 			// Get issue count from direct store
 			if store != nil {
 				ctx := context.Background()
+
+				// Check database freshness before reading (bd-2q6d, bd-c4rq)
+				// Skip check when using daemon (daemon auto-imports on staleness)
+				if daemonClient == nil {
+					if err := ensureDatabaseFresh(ctx); err != nil {
+						fmt.Fprintf(os.Stderr, "Error: %v\n", err)
+						os.Exit(1)
+					}
+				}
+
 				filter := types.IssueFilter{}
 				issues, err := store.SearchIssues(ctx, "", filter)
 				if err == nil {

cmd/bd/list.go

@@ -193,6 +193,16 @@ var listCmd = &cobra.Command{
 			filter.PriorityMax = &priorityMax
 		}
 
+		// Check database freshness before reading (bd-2q6d, bd-c4rq)
+		// Skip check when using daemon (daemon auto-imports on staleness)
+		ctx := context.Background()
+		if daemonClient == nil {
+			if err := ensureDatabaseFresh(ctx); err != nil {
+				fmt.Fprintf(os.Stderr, "Error: %v\n", err)
+				os.Exit(1)
+			}
+		}
+
 	// If daemon is running, use RPC
 		if daemonClient != nil {
 			listArgs := &rpc.ListArgs{
@@ -310,7 +320,7 @@ var listCmd = &cobra.Command{
 		}
 
 		// Direct mode
-		ctx := context.Background()
+		// ctx already created above for staleness check
 		issues, err := store.SearchIssues(ctx, "", filter)
 		if err != nil {
 		fmt.Fprintf(os.Stderr, "Error: %v\n", err)

cmd/bd/ready.go

@@ -98,6 +98,16 @@ var readyCmd = &cobra.Command{
 		}
 		// Direct mode
 		ctx := context.Background()
+
+		// Check database freshness before reading (bd-2q6d, bd-c4rq)
+		// Skip check when using daemon (daemon auto-imports on staleness)
+		if daemonClient == nil {
+			if err := ensureDatabaseFresh(ctx); err != nil {
+				fmt.Fprintf(os.Stderr, "Error: %v\n", err)
+				os.Exit(1)
+			}
+		}
+
 		issues, err := store.GetReadyWork(ctx, filter)
 		if err != nil {
 		fmt.Fprintf(os.Stderr, "Error: %v\n", err)

cmd/bd/show.go

@@ -24,6 +24,15 @@ var showCmd = &cobra.Command{
 		jsonOutput, _ := cmd.Flags().GetBool("json")
 		ctx := context.Background()
 
+		// Check database freshness before reading (bd-2q6d, bd-c4rq)
+		// Skip check when using daemon (daemon auto-imports on staleness)
+		if daemonClient == nil {
+			if err := ensureDatabaseFresh(ctx); err != nil {
+				fmt.Fprintf(os.Stderr, "Error: %v\n", err)
+				os.Exit(1)
+			}
+		}
+
 		// Resolve partial IDs first
 		var resolvedIDs []string
 		if daemonClient != nil {

cmd/bd/stale.go

@@ -62,6 +62,16 @@ This helps identify:
 		}
 		// Direct mode
 		ctx := context.Background()
+
+		// Check database freshness before reading (bd-2q6d, bd-c4rq)
+		// Skip check when using daemon (daemon auto-imports on staleness)
+		if daemonClient == nil {
+			if err := ensureDatabaseFresh(ctx); err != nil {
+				fmt.Fprintf(os.Stderr, "Error: %v\n", err)
+				os.Exit(1)
+			}
+		}
+
 		issues, err := store.GetStaleIssues(ctx, filter)
 		if err != nil {
 			fmt.Fprintf(os.Stderr, "Error: %v\n", err)

cmd/bd/staleness.go

@@ -0,0 +1,51 @@
+package main
+
+import (
+	"context"
+	"fmt"
+	"os"
+
+	"github.com/steveyegge/beads/internal/autoimport"
+)
+
+// ensureDatabaseFresh checks if the database is in sync with JSONL before read operations.
+// If JSONL is newer than database, refuses to operate with an error message.
+// This prevents users from making decisions based on stale/incomplete data.
+//
+// NOTE: Callers must check if daemonClient != nil and skip calling this function
+// when running in daemon mode (daemon auto-imports on staleness).
+//
+// Implements bd-2q6d: All read operations should validate database freshness.
+// Implements bd-c4rq: Daemon check moved to call sites to avoid function call overhead.
+func ensureDatabaseFresh(ctx context.Context) error {
+	// Skip check if no storage available (shouldn't happen in practice)
+	if store == nil {
+		return nil
+	}
+
+	// Check if database is stale
+	isStale, err := autoimport.CheckStaleness(ctx, store, dbPath)
+	if err != nil {
+		// If we can't determine staleness, allow operation to proceed
+		// (better to show potentially stale data than block user)
+		fmt.Fprintf(os.Stderr, "Warning: could not check database staleness: %v\n", err)
+		return nil
+	}
+
+	if !isStale {
+		// Database is fresh, proceed
+		return nil
+	}
+
+	// Database is stale - refuse to operate
+	return fmt.Errorf(
+		"Database out of sync with JSONL. Run 'bd import' first.\n\n"+
+			"The JSONL file has been updated (e.g., after 'git pull') but the database\n"+
+			"hasn't been imported yet. This would cause you to see stale/incomplete data.\n\n"+
+			"To fix:\n"+
+			"  bd import        # Import JSONL updates to database\n\n"+
+			"Or use daemon mode (auto-imports on every operation):\n"+
+			"  bd daemon start\n"+
+			"  bd <command>     # Will auto-import before executing",
+	)
+}

cmd/bd/status.go

@@ -77,6 +77,16 @@ Examples:
 		var stats *types.Statistics
 		var err error
 
+		// Check database freshness before reading (bd-2q6d, bd-c4rq)
+		// Skip check when using daemon (daemon auto-imports on staleness)
+		ctx := context.Background()
+		if daemonClient == nil {
+			if err := ensureDatabaseFresh(ctx); err != nil {
+				fmt.Fprintf(os.Stderr, "Error: %v\n", err)
+				os.Exit(1)
+			}
+		}
+
 		// If daemon is running, use RPC
 		if daemonClient != nil {
 			resp, rpcErr := daemonClient.Stats()

cmd/bd/validate.go

@@ -34,6 +34,16 @@ Example:
 		checksFlag, _ := cmd.Flags().GetString("checks")
 		jsonOut, _ := cmd.Flags().GetBool("json")
 		ctx := context.Background()
+
+		// Check database freshness before reading (bd-2q6d, bd-c4rq)
+		// Skip check when using daemon (daemon auto-imports on staleness)
+		if daemonClient == nil {
+			if err := ensureDatabaseFresh(ctx); err != nil {
+				fmt.Fprintf(os.Stderr, "Error: %v\n", err)
+				os.Exit(1)
+			}
+		}
+
 		// Parse and normalize checks
 		checks, err := parseChecks(checksFlag)
 		if err != nil {

internal/autoimport/autoimport.go

@@ -250,36 +250,49 @@ func parseJSONL(jsonlData []byte, _ Notifier) ([]*types.Issue, error) {
 
 // CheckStaleness checks if JSONL is newer than last import
 // dbPath is the full path to the database file
+//
+// Returns:
+//   - (true, nil) if JSONL is newer than last import (database is stale)
+//   - (false, nil) if database is fresh or no JSONL exists yet
+//   - (false, err) if an abnormal error occurred (file system issues, permissions, etc.)
 func CheckStaleness(ctx context.Context, store storage.Storage, dbPath string) (bool, error) {
 	lastImportStr, err := store.GetMetadata(ctx, "last_import_time")
 	if err != nil {
+		// No metadata yet - expected for first run
 		return false, nil
 	}
-	
+
 	lastImportTime, err := time.Parse(time.RFC3339, lastImportStr)
 	if err != nil {
+		// Corrupted metadata - not critical, assume not stale
 		return false, nil
 	}
-	
+
 	// Find JSONL using database directory
 	dbDir := filepath.Dir(dbPath)
 	pattern := filepath.Join(dbDir, "*.jsonl")
 	matches, err := filepath.Glob(pattern)
+	if err != nil {
+		// Glob failed - this is abnormal
+		return false, fmt.Errorf("failed to find JSONL file: %w", err)
+	}
+
 	var jsonlPath string
-	if err == nil && len(matches) > 0 {
+	if len(matches) > 0 {
 		jsonlPath = matches[0]
 	} else {
 		jsonlPath = filepath.Join(dbDir, "issues.jsonl")
 	}
-	
-	if jsonlPath == "" {
-		return false, nil
-	}
-	
+
 	stat, err := os.Stat(jsonlPath)
 	if err != nil {
-		return false, nil
+		if os.IsNotExist(err) {
+			// JSONL doesn't exist - expected for new repo
+			return false, nil
+		}
+		// Other stat error (permissions, etc.) - abnormal
+		return false, fmt.Errorf("failed to stat JSONL file %s: %w", jsonlPath, err)
 	}
-	
+
 	return stat.ModTime().After(lastImportTime), nil
 }

internal/rpc/server_export_import_auto.go

@@ -184,8 +184,13 @@ func (s *Server) checkAndAutoImportIfStale(req *Request) error {
 	// Fast path: Check if JSONL is stale using cheap mtime check
 	// This avoids reading/hashing JSONL on every request
 	isStale, err := autoimport.CheckStaleness(ctx, store, dbPath)
-	if err != nil || !isStale {
-		return err
+	if err != nil {
+		// Log error but allow request to proceed (don't block on staleness check failure)
+		fmt.Fprintf(os.Stderr, "Warning: failed to check staleness: %v\n", err)
+		return nil
+	}
+	if !isStale {
+		return nil
 	}
 
 	// Single-flight guard: Only allow one import at a time
@@ -220,8 +225,13 @@ func (s *Server) checkAndAutoImportIfStale(req *Request) error {
 
 	// Double-check staleness after acquiring lock (another goroutine may have imported)
 	isStale, err = autoimport.CheckStaleness(ctx, store, dbPath)
-	if err != nil || !isStale {
-		return err
+	if err != nil {
+		// Log error but allow request to proceed (don't block on staleness check failure)
+		fmt.Fprintf(os.Stderr, "Warning: failed to check staleness: %v\n", err)
+		return nil
+	}
+	if !isStale {
+		return nil
 	}
 
 	// Create timeout context for import operation (bd-8931, bd-1048)