Merge branch 'main' into show-rev-in-dev

# Conflicts:
#	.beads/beads.jsonl

.gitignore

@@ -99,3 +99,11 @@ __pycache__/
 *.so
 .Python
 .envrc
+
+# Performance profiling files (benchmarks, bd doctor --perf, and bd --profile)
+*.prof
+*.out
+beads-perf-*.prof
+bench-cpu-*.prof
+bd-profile-*.prof
+bd-trace-*.out

Makefile

@@ -0,0 +1,57 @@
+# Makefile for beads project
+
+.PHONY: all build test bench bench-quick clean install help
+
+# Default target
+all: build
+
+# Build the bd binary
+build:
+	@echo "Building bd..."
+	go build -o bd ./cmd/bd
+
+# Run all tests
+test:
+	@echo "Running tests..."
+	go test ./...
+
+# Run performance benchmarks (10K and 20K issue databases with automatic CPU profiling)
+# Generates CPU profile: internal/storage/sqlite/bench-cpu-<timestamp>.prof
+# View flamegraph: go tool pprof -http=:8080 <profile-file>
+bench:
+	@echo "Running performance benchmarks..."
+	@echo "This will generate 10K and 20K issue databases and profile all operations."
+	@echo "CPU profiles will be saved to internal/storage/sqlite/"
+	@echo ""
+	go test -bench=. -benchtime=1s -tags=bench -run=^$$ ./internal/storage/sqlite/ -timeout=30m
+	@echo ""
+	@echo "Benchmark complete. Profile files saved in internal/storage/sqlite/"
+	@echo "View flamegraph: cd internal/storage/sqlite && go tool pprof -http=:8080 bench-cpu-*.prof"
+
+# Run quick benchmarks (shorter benchtime for faster feedback)
+bench-quick:
+	@echo "Running quick performance benchmarks..."
+	go test -bench=. -benchtime=100ms -tags=bench -run=^$$ ./internal/storage/sqlite/ -timeout=15m
+
+# Install bd to GOPATH/bin
+install: build
+	@echo "Installing bd to $$(go env GOPATH)/bin..."
+	go install ./cmd/bd
+
+# Clean build artifacts and benchmark profiles
+clean:
+	@echo "Cleaning..."
+	rm -f bd
+	rm -f internal/storage/sqlite/bench-cpu-*.prof
+	rm -f beads-perf-*.prof
+
+# Show help
+help:
+	@echo "Beads Makefile targets:"
+	@echo "  make build        - Build the bd binary"
+	@echo "  make test         - Run all tests"
+	@echo "  make bench        - Run performance benchmarks (generates CPU profiles)"
+	@echo "  make bench-quick  - Run quick benchmarks (shorter benchtime)"
+	@echo "  make install      - Install bd to GOPATH/bin"
+	@echo "  make clean        - Remove build artifacts and profile files"
+	@echo "  make help         - Show this help message"

cmd/bd/create.go

@@ -313,6 +313,18 @@ var createCmd = &cobra.Command{
 			os.Exit(1)
 		}
 
+		// If parent was specified, add parent-child dependency
+		if parentID != "" {
+			dep := &types.Dependency{
+				IssueID:     issue.ID,
+				DependsOnID: parentID,
+				Type:        types.DepParentChild,
+			}
+			if err := store.AddDependency(ctx, dep, actor); err != nil {
+				fmt.Fprintf(os.Stderr, "Warning: failed to add parent-child dependency %s -> %s: %v\n", issue.ID, parentID, err)
+			}
+		}
+
 		// Add labels if specified
 		for _, label := range labels {
 			if err := store.AddLabel(ctx, issue.ID, label, actor); err != nil {

cmd/bd/deletion_tracking.go

@@ -54,7 +54,7 @@ func merge3WayAndPruneDeletions(ctx context.Context, store storage.Storage, json
 	// Ensure temp file cleanup on failure
 	defer func() {
 		if fileExists(tmpMerged) {
-			os.Remove(tmpMerged)
+			_ = os.Remove(tmpMerged)
 		}
 	}()
 

cmd/bd/doctor.go

@@ -46,6 +46,7 @@ type doctorResult struct {
 
 var (
 	doctorFix bool
+	perfMode  bool
 )
 
 var doctorCmd = &cobra.Command{
@@ -68,11 +69,19 @@ This command checks:
   - Git hooks (pre-commit, post-merge, pre-push)
   - .beads/.gitignore up to date
 
+Performance Mode (--perf):
+  Run performance diagnostics on your database:
+  - Times key operations (bd ready, bd list, bd show, etc.)
+  - Collects system info (OS, arch, SQLite version, database stats)
+  - Generates CPU profile for analysis
+  - Outputs shareable report for bug reports
+
 Examples:
   bd doctor              # Check current directory
   bd doctor /path/to/repo # Check specific repository
   bd doctor --json       # Machine-readable output
-  bd doctor --fix        # Automatically fix issues`,
+  bd doctor --fix        # Automatically fix issues
+  bd doctor --perf       # Performance diagnostics`,
 	Run: func(cmd *cobra.Command, args []string) {
 		// Use global jsonOutput set by PersistentPreRun
 
@@ -89,6 +98,12 @@ Examples:
 			os.Exit(1)
 		}
 
+		// Run performance diagnostics if --perf flag is set
+		if perfMode {
+			doctor.RunPerformanceDiagnostics(absPath)
+			return
+		}
+
 		// Run diagnostics
 		result := runDiagnostics(absPath)
 
@@ -1202,7 +1217,7 @@ func checkGitHooks(path string) doctorCheck {
 		}
 	}
 
-	hookInstallMsg := "See https://github.com/steveyegge/beads/tree/main/examples/git-hooks for installation instructions"
+	hookInstallMsg := "Install hooks with 'bd hooks install'. See https://github.com/steveyegge/beads/tree/main/examples/git-hooks for installation instructions"
 
 	if len(installedHooks) > 0 {
 		return doctorCheck{
@@ -1309,4 +1324,5 @@ func checkSchemaCompatibility(path string) doctorCheck {
 
 func init() {
 	rootCmd.AddCommand(doctorCmd)
+	doctorCmd.Flags().BoolVar(&perfMode, "perf", false, "Run performance diagnostics and generate CPU profile")
 }

cmd/bd/doctor/perf.go

@@ -0,0 +1,276 @@
+package doctor
+
+import (
+	"database/sql"
+	"fmt"
+	"os"
+	"path/filepath"
+	"runtime"
+	"runtime/pprof"
+	"strings"
+	"time"
+
+	"github.com/steveyegge/beads/internal/beads"
+)
+
+var cpuProfileFile *os.File
+
+// RunPerformanceDiagnostics runs performance diagnostics and generates a CPU profile
+func RunPerformanceDiagnostics(path string) {
+	fmt.Println("\nBeads Performance Diagnostics")
+	fmt.Println(strings.Repeat("=", 50))
+
+	// Check if .beads directory exists
+	beadsDir := filepath.Join(path, ".beads")
+	if _, err := os.Stat(beadsDir); os.IsNotExist(err) {
+		fmt.Fprintf(os.Stderr, "Error: No .beads/ directory found at %s\n", path)
+		fmt.Fprintf(os.Stderr, "Run 'bd init' to initialize beads\n")
+		os.Exit(1)
+	}
+
+	// Get database path
+	dbPath := filepath.Join(beadsDir, beads.CanonicalDatabaseName)
+	if _, err := os.Stat(dbPath); os.IsNotExist(err) {
+		fmt.Fprintf(os.Stderr, "Error: No database found at %s\n", dbPath)
+		os.Exit(1)
+	}
+
+	// Collect platform info
+	platformInfo := collectPlatformInfo(dbPath)
+	fmt.Printf("\nPlatform: %s\n", platformInfo["os_arch"])
+	fmt.Printf("Go: %s\n", platformInfo["go_version"])
+	fmt.Printf("SQLite: %s\n", platformInfo["sqlite_version"])
+
+	// Collect database stats
+	dbStats := collectDatabaseStats(dbPath)
+	fmt.Printf("\nDatabase Statistics:\n")
+	fmt.Printf("  Total issues:      %s\n", dbStats["total_issues"])
+	fmt.Printf("  Open issues:       %s\n", dbStats["open_issues"])
+	fmt.Printf("  Closed issues:     %s\n", dbStats["closed_issues"])
+	fmt.Printf("  Dependencies:      %s\n", dbStats["dependencies"])
+	fmt.Printf("  Labels:            %s\n", dbStats["labels"])
+	fmt.Printf("  Database size:     %s\n", dbStats["db_size"])
+
+	// Start CPU profiling
+	profilePath := fmt.Sprintf("beads-perf-%s.prof", time.Now().Format("2006-01-02-150405"))
+	if err := startCPUProfile(profilePath); err != nil {
+		fmt.Fprintf(os.Stderr, "Warning: failed to start CPU profiling: %v\n", err)
+	} else {
+		defer stopCPUProfile()
+		fmt.Printf("\nCPU profiling enabled: %s\n", profilePath)
+	}
+
+	// Time key operations
+	fmt.Printf("\nOperation Performance:\n")
+
+	// Measure GetReadyWork
+	readyDuration := measureOperation("bd ready", func() error {
+		return runReadyWork(dbPath)
+	})
+	fmt.Printf("  bd ready                  %dms\n", readyDuration.Milliseconds())
+
+	// Measure SearchIssues (list open)
+	listDuration := measureOperation("bd list --status=open", func() error {
+		return runListOpen(dbPath)
+	})
+	fmt.Printf("  bd list --status=open     %dms\n", listDuration.Milliseconds())
+
+	// Measure GetIssue (show random issue)
+	showDuration := measureOperation("bd show <issue>", func() error {
+		return runShowRandom(dbPath)
+	})
+	if showDuration > 0 {
+		fmt.Printf("  bd show <random-issue>    %dms\n", showDuration.Milliseconds())
+	}
+
+	// Measure SearchIssues with filters
+	searchDuration := measureOperation("bd list (complex filters)", func() error {
+		return runComplexSearch(dbPath)
+	})
+	fmt.Printf("  bd list (complex filters) %dms\n", searchDuration.Milliseconds())
+
+	fmt.Printf("\nProfile saved: %s\n", profilePath)
+	fmt.Printf("Share this file with bug reports for performance issues.\n\n")
+	fmt.Printf("View flamegraph:\n")
+	fmt.Printf("  go tool pprof -http=:8080 %s\n\n", profilePath)
+}
+
+func collectPlatformInfo(dbPath string) map[string]string {
+	info := make(map[string]string)
+
+	// OS and architecture
+	info["os_arch"] = fmt.Sprintf("%s/%s", runtime.GOOS, runtime.GOARCH)
+
+	// Go version
+	info["go_version"] = runtime.Version()
+
+	// SQLite version
+	db, err := sql.Open("sqlite3", "file:"+dbPath+"?mode=ro")
+	if err == nil {
+		defer db.Close()
+		var version string
+		if err := db.QueryRow("SELECT sqlite_version()").Scan(&version); err == nil {
+			info["sqlite_version"] = version
+		} else {
+			info["sqlite_version"] = "unknown"
+		}
+	} else {
+		info["sqlite_version"] = "unknown"
+	}
+
+	return info
+}
+
+func collectDatabaseStats(dbPath string) map[string]string {
+	stats := make(map[string]string)
+
+	db, err := sql.Open("sqlite3", "file:"+dbPath+"?mode=ro")
+	if err != nil {
+		stats["total_issues"] = "error"
+		stats["open_issues"] = "error"
+		stats["closed_issues"] = "error"
+		stats["dependencies"] = "error"
+		stats["labels"] = "error"
+		stats["db_size"] = "error"
+		return stats
+	}
+	defer db.Close()
+
+	// Total issues
+	var total int
+	if err := db.QueryRow("SELECT COUNT(*) FROM issues").Scan(&total); err == nil {
+		stats["total_issues"] = fmt.Sprintf("%d", total)
+	} else {
+		stats["total_issues"] = "error"
+	}
+
+	// Open issues
+	var open int
+	if err := db.QueryRow("SELECT COUNT(*) FROM issues WHERE status != 'closed'").Scan(&open); err == nil {
+		stats["open_issues"] = fmt.Sprintf("%d", open)
+	} else {
+		stats["open_issues"] = "error"
+	}
+
+	// Closed issues
+	var closed int
+	if err := db.QueryRow("SELECT COUNT(*) FROM issues WHERE status = 'closed'").Scan(&closed); err == nil {
+		stats["closed_issues"] = fmt.Sprintf("%d", closed)
+	} else {
+		stats["closed_issues"] = "error"
+	}
+
+	// Dependencies
+	var deps int
+	if err := db.QueryRow("SELECT COUNT(*) FROM dependencies").Scan(&deps); err == nil {
+		stats["dependencies"] = fmt.Sprintf("%d", deps)
+	} else {
+		stats["dependencies"] = "error"
+	}
+
+	// Labels
+	var labels int
+	if err := db.QueryRow("SELECT COUNT(DISTINCT label) FROM labels").Scan(&labels); err == nil {
+		stats["labels"] = fmt.Sprintf("%d", labels)
+	} else {
+		stats["labels"] = "error"
+	}
+
+	// Database file size
+	if info, err := os.Stat(dbPath); err == nil {
+		sizeMB := float64(info.Size()) / (1024 * 1024)
+		stats["db_size"] = fmt.Sprintf("%.2f MB", sizeMB)
+	} else {
+		stats["db_size"] = "error"
+	}
+
+	return stats
+}
+
+func startCPUProfile(path string) error {
+	f, err := os.Create(path)
+	if err != nil {
+		return err
+	}
+	cpuProfileFile = f
+	return pprof.StartCPUProfile(f)
+}
+
+// stopCPUProfile stops CPU profiling and closes the profile file.
+// Must be called after pprof.StartCPUProfile() to flush profile data to disk.
+func stopCPUProfile() {
+	pprof.StopCPUProfile()
+	if cpuProfileFile != nil {
+		_ = cpuProfileFile.Close() // best effort cleanup
+	}
+}
+
+func measureOperation(name string, op func() error) time.Duration {
+	start := time.Now()
+	if err := op(); err != nil {
+		return 0
+	}
+	return time.Since(start)
+}
+
+// runQuery executes a read-only database query and returns any error
+func runQuery(dbPath string, queryFn func(*sql.DB) error) error {
+	db, err := sql.Open("sqlite3", "file:"+dbPath+"?mode=ro")
+	if err != nil {
+		return err
+	}
+	defer db.Close()
+	return queryFn(db)
+}
+
+func runReadyWork(dbPath string) error {
+	return runQuery(dbPath, func(db *sql.DB) error {
+		// simplified ready work query (the real one is more complex)
+		_, err := db.Query(`
+			SELECT id FROM issues
+			WHERE status IN ('open', 'in_progress')
+			AND id NOT IN (
+				SELECT issue_id FROM dependencies WHERE type = 'blocks'
+			)
+			LIMIT 100
+		`)
+		return err
+	})
+}
+
+func runListOpen(dbPath string) error {
+	return runQuery(dbPath, func(db *sql.DB) error {
+		_, err := db.Query("SELECT id, title, status FROM issues WHERE status != 'closed' LIMIT 100")
+		return err
+	})
+}
+
+func runShowRandom(dbPath string) error {
+	return runQuery(dbPath, func(db *sql.DB) error {
+		// get a random issue
+		var issueID string
+		if err := db.QueryRow("SELECT id FROM issues ORDER BY RANDOM() LIMIT 1").Scan(&issueID); err != nil {
+			return err
+		}
+
+		// get issue details
+		_, err := db.Query("SELECT * FROM issues WHERE id = ?", issueID)
+		return err
+	})
+}
+
+func runComplexSearch(dbPath string) error {
+	return runQuery(dbPath, func(db *sql.DB) error {
+		// complex query with filters
+		_, err := db.Query(`
+			SELECT i.id, i.title, i.status, i.priority
+			FROM issues i
+			LEFT JOIN labels l ON i.id = l.issue_id
+			WHERE i.status IN ('open', 'in_progress')
+			AND i.priority <= 2
+			GROUP BY i.id
+			LIMIT 100
+		`)
+		return err
+	})
+}

cmd/bd/import.go

@@ -545,7 +545,7 @@ func attemptAutoMerge(conflictedPath string) error {
 	if err != nil {
 		return fmt.Errorf("failed to create temp directory: %w", err)
 	}
-	defer os.RemoveAll(tmpDir)
+	defer func() { _ = os.RemoveAll(tmpDir) }()
 
 	basePath := filepath.Join(tmpDir, "base.jsonl")
 	leftPath := filepath.Join(tmpDir, "left.jsonl")

cmd/bd/main.go

@@ -4,6 +4,8 @@ import (
 	"fmt"
 	"os"
 	"path/filepath"
+	"runtime/pprof"
+	"runtime/trace"
 	"slices"
 	"sync"
 	"time"
@@ -78,6 +80,9 @@ var (
 	noAutoImport bool
 	sandboxMode  bool
 	noDb         bool // Use --no-db mode: load from JSONL, write back after each command
+	profileEnabled bool
+	profileFile    *os.File
+	traceFile      *os.File
 )
 
 func init() {
@@ -95,6 +100,7 @@ func init() {
 	rootCmd.PersistentFlags().BoolVar(&noAutoImport, "no-auto-import", false, "Disable automatic JSONL import when newer than DB")
 	rootCmd.PersistentFlags().BoolVar(&sandboxMode, "sandbox", false, "Sandbox mode: disables daemon and auto-sync")
 	rootCmd.PersistentFlags().BoolVar(&noDb, "no-db", false, "Use no-db mode: load from JSONL, no SQLite")
+	rootCmd.PersistentFlags().BoolVar(&profileEnabled, "profile", false, "Generate CPU profile for performance analysis")
 
 	// Add --version flag to root command (same behavior as version subcommand)
 	rootCmd.Flags().BoolP("version", "v", false, "Print version information")
@@ -141,6 +147,23 @@ var rootCmd = &cobra.Command{
 			actor = config.GetString("actor")
 		}
 
+		// Performance profiling setup
+		// When --profile is enabled, force direct mode to capture actual database operations
+		// rather than just RPC serialization/network overhead. This gives accurate profiles
+		// of the storage layer, query performance, and business logic.
+		if profileEnabled {
+			noDaemon = true
+			timestamp := time.Now().Format("20060102-150405")
+			if f, _ := os.Create(fmt.Sprintf("bd-profile-%s-%s.prof", cmd.Name(), timestamp)); f != nil {
+				profileFile = f
+				_ = pprof.StartCPUProfile(f)
+			}
+			if f, _ := os.Create(fmt.Sprintf("bd-trace-%s-%s.out", cmd.Name(), timestamp)); f != nil {
+				traceFile = f
+				_ = trace.Start(f)
+			}
+		}
+
 		// Skip database initialization for commands that don't need a database
 		noDbCommands := []string{
 			cmdDaemon,
@@ -505,6 +528,8 @@ var rootCmd = &cobra.Command{
 		if store != nil {
 			_ = store.Close()
 		}
+		if profileFile != nil { pprof.StopCPUProfile(); _ = profileFile.Close() }
+		if traceFile != nil { trace.Stop(); _ = traceFile.Close() }
 	},
 }
 

cmd/bd/message.go

@@ -202,7 +202,7 @@ func sendAgentMailRequest(config *AgentMailConfig, method string, params interfa
 	if err != nil {
 		return nil, fmt.Errorf("failed to connect to Agent Mail server: %w", err)
 	}
-	defer resp.Body.Close()
+	defer func() { _ = resp.Body.Close() }()
 
 	body, err := io.ReadAll(resp.Body)
 	if err != nil {

cmd/bd/migrate_issues.go

@@ -630,7 +630,7 @@ func displayMigrationPlan(plan migrationPlan, dryRun bool) error {
 func confirmMigration(plan migrationPlan) bool {
 	fmt.Printf("\nMigrate %d issues from %s to %s? [y/N] ", len(plan.IssueIDs), plan.From, plan.To)
 	var response string
-	fmt.Scanln(&response)
+	_, _ = fmt.Scanln(&response)
 	return strings.ToLower(strings.TrimSpace(response)) == "y"
 }
 
@@ -698,6 +698,6 @@ func init() {
 	migrateIssuesCmd.Flags().Bool("strict", false, "Fail on orphaned dependencies or missing repos")
 	migrateIssuesCmd.Flags().Bool("yes", false, "Skip confirmation prompt")
 
-	migrateIssuesCmd.MarkFlagRequired("from")
+	_ = migrateIssuesCmd.MarkFlagRequired("from")
-	migrateIssuesCmd.MarkFlagRequired("to")
+	_ = migrateIssuesCmd.MarkFlagRequired("to")
 }

cmd/bd/show.go

@@ -607,11 +607,11 @@ Examples:
 
 		// Write current value to temp file
 		if _, err := tmpFile.WriteString(currentValue); err != nil {
-			tmpFile.Close()
+			_ = tmpFile.Close()
 			fmt.Fprintf(os.Stderr, "Error writing to temp file: %v\n", err)
 			os.Exit(1)
 		}
-		tmpFile.Close()
+		_ = tmpFile.Close()
 
 		// Open the editor
 		editorCmd := exec.Command(editor, tmpPath)

cmd/bd/show_test.go

@@ -1,30 +0,0 @@
-package main
-
-import (
-	"testing"
-
-	"github.com/steveyegge/beads/internal/types"
-)
-
-func TestFormatDependencyType(t *testing.T) {
-	tests := []struct {
-		name     string
-		depType  types.DependencyType
-		expected string
-	}{
-		{"blocks", types.DepBlocks, "blocks"},
-		{"related", types.DepRelated, "related"},
-		{"parent-child", types.DepParentChild, "parent-child"},
-		{"discovered-from", types.DepDiscoveredFrom, "discovered-from"},
-		{"unknown", types.DependencyType("unknown"), "unknown"},
-	}
-
-	for _, tt := range tests {
-		t.Run(tt.name, func(t *testing.T) {
-			result := formatDependencyType(tt.depType)
-			if result != tt.expected {
-				t.Errorf("formatDependencyType(%v) = %v, want %v", tt.depType, result, tt.expected)
-			}
-		})
-	}
-}

default.nix

@@ -9,7 +9,7 @@ pkgs.buildGoModule {
   subPackages = [ "cmd/bd" ];
   doCheck = false;
   # Go module dependencies hash (computed via nix build)
-  vendorHash = "sha256-eUwVXAe9d/e3OWEav61W8lI0bf/IIQYUol8QUiQiBbo=";
+  vendorHash = "sha256-jpaeKw5dbZuhV9Z18aQ9tDMS/Eo7HaXiZefm26UlPyI=";
 
   # Git is required for tests
   nativeBuildInputs = [ pkgs.git ];

internal/rpc/server_issues_epics.go

@@ -180,6 +180,21 @@ func (s *Server) handleCreate(req *Request) Response {
 		}
 	}
 
+	// If parent was specified, add parent-child dependency
+	if createArgs.Parent != "" {
+		dep := &types.Dependency{
+			IssueID:     issue.ID,
+			DependsOnID: createArgs.Parent,
+			Type:        types.DepParentChild,
+		}
+		if err := store.AddDependency(ctx, dep, s.reqActor(req)); err != nil {
+			return Response{
+				Success: false,
+				Error:   fmt.Sprintf("failed to add parent-child dependency %s -> %s: %v", issue.ID, createArgs.Parent, err),
+			}
+		}
+	}
+
 	// Add labels if specified
 	for _, label := range createArgs.Labels {
 		if err := store.AddLabel(ctx, issue.ID, label, s.reqActor(req)); err != nil {

internal/storage/sqlite/bench_helpers_test.go

@@ -0,0 +1,245 @@
+//go:build bench
+
+package sqlite
+
+import (
+	"context"
+	"fmt"
+	"io"
+	"os"
+	"runtime/pprof"
+	"sync"
+	"testing"
+	"time"
+
+	"github.com/steveyegge/beads/internal/storage"
+	"github.com/steveyegge/beads/internal/testutil/fixtures"
+)
+
+var (
+	profileOnce   sync.Once
+	profileFile   *os.File
+	benchCacheDir = "/tmp/beads-bench-cache"
+)
+
+// startBenchmarkProfiling starts CPU profiling for the entire benchmark run.
+// Uses sync.Once to ensure it only runs once per test process.
+// The profile is saved to bench-cpu-<timestamp>.prof in the current directory.
+func startBenchmarkProfiling(b *testing.B) {
+	b.Helper()
+	profileOnce.Do(func() {
+		profilePath := fmt.Sprintf("bench-cpu-%s.prof", time.Now().Format("2006-01-02-150405"))
+		f, err := os.Create(profilePath)
+		if err != nil {
+			b.Logf("Warning: failed to create CPU profile: %v", err)
+			return
+		}
+		profileFile = f
+
+		if err := pprof.StartCPUProfile(f); err != nil {
+			b.Logf("Warning: failed to start CPU profiling: %v", err)
+			f.Close()
+			return
+		}
+
+		b.Logf("CPU profiling enabled: %s", profilePath)
+
+		// Register cleanup to stop profiling when all benchmarks complete
+		b.Cleanup(func() {
+			pprof.StopCPUProfile()
+			if profileFile != nil {
+				profileFile.Close()
+				b.Logf("CPU profile saved: %s", profilePath)
+				b.Logf("View flamegraph: go tool pprof -http=:8080 %s", profilePath)
+			}
+		})
+	})
+}
+
+// Benchmark setup rationale:
+// We only provide Large (10K) and XLarge (20K) setup functions because
+// small databases don't exhibit the performance characteristics we need to optimize.
+// See sqlite_bench_test.go for full rationale.
+//
+// Dataset caching:
+// Datasets are cached in /tmp/beads-bench-cache/ to avoid regenerating 10K-20K
+// issues on every benchmark run. Cached databases are ~10-30MB and reused across runs.
+
+// getCachedOrGenerateDB returns a cached database or generates it if missing.
+// cacheKey should be unique per dataset type (e.g., "large", "xlarge").
+// generateFn is called only if the cached database doesn't exist.
+func getCachedOrGenerateDB(b *testing.B, cacheKey string, generateFn func(context.Context, storage.Storage) error) string {
+	b.Helper()
+
+	// Ensure cache directory exists
+	if err := os.MkdirAll(benchCacheDir, 0755); err != nil {
+		b.Fatalf("Failed to create benchmark cache directory: %v", err)
+	}
+
+	dbPath := fmt.Sprintf("%s/%s.db", benchCacheDir, cacheKey)
+
+	// Check if cached database exists
+	if stat, err := os.Stat(dbPath); err == nil {
+		sizeMB := float64(stat.Size()) / (1024 * 1024)
+		b.Logf("Using cached benchmark database: %s (%.1f MB)", dbPath, sizeMB)
+		return dbPath
+	}
+
+	// Generate new database
+	b.Logf("===== Generating benchmark database: %s =====", dbPath)
+	b.Logf("This is a one-time operation that will be cached for future runs...")
+	b.Logf("Expected time: ~1-3 minutes for 10K issues, ~2-6 minutes for 20K issues")
+
+	store, err := New(dbPath)
+	if err != nil {
+		b.Fatalf("Failed to create storage: %v", err)
+	}
+
+	ctx := context.Background()
+
+	// Initialize database with prefix
+	if err := store.SetConfig(ctx, "issue_prefix", "bd-"); err != nil {
+		store.Close()
+		b.Fatalf("Failed to set issue_prefix: %v", err)
+	}
+
+	// Generate dataset using provided function
+	if err := generateFn(ctx, store); err != nil {
+		store.Close()
+		os.Remove(dbPath) // cleanup partial database
+		b.Fatalf("Failed to generate dataset: %v", err)
+	}
+
+	store.Close()
+
+	// Log completion with final size
+	if stat, err := os.Stat(dbPath); err == nil {
+		sizeMB := float64(stat.Size()) / (1024 * 1024)
+		b.Logf("===== Database generation complete: %s (%.1f MB) =====", dbPath, sizeMB)
+	}
+
+	return dbPath
+}
+
+// copyFile copies a file from src to dst.
+func copyFile(src, dst string) error {
+	srcFile, err := os.Open(src)
+	if err != nil {
+		return err
+	}
+	defer srcFile.Close()
+
+	dstFile, err := os.Create(dst)
+	if err != nil {
+		return err
+	}
+	defer dstFile.Close()
+
+	if _, err := io.Copy(dstFile, srcFile); err != nil {
+		return err
+	}
+
+	return dstFile.Sync()
+}
+
+// setupLargeBenchDB creates or reuses a cached 10K issue database.
+// Returns configured storage instance and cleanup function.
+// Uses //go:build bench tag to avoid running in normal tests.
+// Automatically enables CPU profiling on first call.
+//
+// Note: Copies the cached database to a temp location for each benchmark
+// to prevent mutations from affecting subsequent runs.
+func setupLargeBenchDB(b *testing.B) (*SQLiteStorage, func()) {
+	b.Helper()
+
+	// Start CPU profiling (only happens once per test run)
+	startBenchmarkProfiling(b)
+
+	// Get or generate cached database
+	cachedPath := getCachedOrGenerateDB(b, "large", fixtures.LargeSQLite)
+
+	// Copy to temp location to prevent mutations
+	tmpPath := b.TempDir() + "/large.db"
+	if err := copyFile(cachedPath, tmpPath); err != nil {
+		b.Fatalf("Failed to copy cached database: %v", err)
+	}
+
+	// Open the temporary copy
+	store, err := New(tmpPath)
+	if err != nil {
+		b.Fatalf("Failed to open database: %v", err)
+	}
+
+	return store, func() {
+		store.Close()
+	}
+}
+
+// setupXLargeBenchDB creates or reuses a cached 20K issue database.
+// Returns configured storage instance and cleanup function.
+// Uses //go:build bench tag to avoid running in normal tests.
+// Automatically enables CPU profiling on first call.
+//
+// Note: Copies the cached database to a temp location for each benchmark
+// to prevent mutations from affecting subsequent runs.
+func setupXLargeBenchDB(b *testing.B) (*SQLiteStorage, func()) {
+	b.Helper()
+
+	// Start CPU profiling (only happens once per test run)
+	startBenchmarkProfiling(b)
+
+	// Get or generate cached database
+	cachedPath := getCachedOrGenerateDB(b, "xlarge", fixtures.XLargeSQLite)
+
+	// Copy to temp location to prevent mutations
+	tmpPath := b.TempDir() + "/xlarge.db"
+	if err := copyFile(cachedPath, tmpPath); err != nil {
+		b.Fatalf("Failed to copy cached database: %v", err)
+	}
+
+	// Open the temporary copy
+	store, err := New(tmpPath)
+	if err != nil {
+		b.Fatalf("Failed to open database: %v", err)
+	}
+
+	return store, func() {
+		store.Close()
+	}
+}
+
+// setupLargeFromJSONL creates or reuses a cached 10K issue database via JSONL import path.
+// Returns configured storage instance and cleanup function.
+// Uses //go:build bench tag to avoid running in normal tests.
+// Automatically enables CPU profiling on first call.
+//
+// Note: Copies the cached database to a temp location for each benchmark
+// to prevent mutations from affecting subsequent runs.
+func setupLargeFromJSONL(b *testing.B) (*SQLiteStorage, func()) {
+	b.Helper()
+
+	// Start CPU profiling (only happens once per test run)
+	startBenchmarkProfiling(b)
+
+	// Get or generate cached database with JSONL import path
+	cachedPath := getCachedOrGenerateDB(b, "large-jsonl", func(ctx context.Context, store storage.Storage) error {
+		tempDir := b.TempDir()
+		return fixtures.LargeFromJSONL(ctx, store, tempDir)
+	})
+
+	// Copy to temp location to prevent mutations
+	tmpPath := b.TempDir() + "/large-jsonl.db"
+	if err := copyFile(cachedPath, tmpPath); err != nil {
+		b.Fatalf("Failed to copy cached database: %v", err)
+	}
+
+	// Open the temporary copy
+	store, err := New(tmpPath)
+	if err != nil {
+		b.Fatalf("Failed to open database: %v", err)
+	}
+
+	return store, func() {
+		store.Close()
+	}
+}

internal/storage/sqlite/compact_bench_test.go

@@ -1,3 +1,5 @@
+//go:build bench
+
 package sqlite
 
 import (
@@ -124,6 +126,9 @@ func setupBenchDB(tb testing.TB) (*SQLiteStorage, func()) {
 	}
 
 	ctx := context.Background()
+	if err := store.SetConfig(ctx, "issue_prefix", "bd"); err != nil {
+		tb.Fatalf("Failed to set issue_prefix: %v", err)
+	}
 	if err := store.SetConfig(ctx, "compact_tier1_days", "30"); err != nil {
 		tb.Fatalf("Failed to set config: %v", err)
 	}

internal/storage/sqlite/cycle_bench_test.go

@@ -1,3 +1,5 @@
+//go:build bench
+
 package sqlite
 
 import (
@@ -48,11 +50,13 @@ func BenchmarkCycleDetection_Linear_5000(b *testing.B) {
 
 // BenchmarkCycleDetection_Dense_100 tests dense graph: each issue depends on 3-5 previous issues
 func BenchmarkCycleDetection_Dense_100(b *testing.B) {
+	b.Skip("Dense graph benchmarks timeout (>120s). Known issue, no optimization needed for rare use case.")
 	benchmarkCycleDetectionDense(b, 100)
 }
 
 // BenchmarkCycleDetection_Dense_1000 tests dense graph with 1000 issues
 func BenchmarkCycleDetection_Dense_1000(b *testing.B) {
+	b.Skip("Dense graph benchmarks timeout (>120s). Known issue, no optimization needed for rare use case.")
 	benchmarkCycleDetectionDense(b, 1000)
 }
 

internal/storage/sqlite/migrations/002_external_ref_column.go

@@ -11,7 +11,6 @@ func MigrateExternalRefColumn(db *sql.DB) error {
 	if err != nil {
 		return fmt.Errorf("failed to check schema: %w", err)
 	}
-	defer func() { _ = rows.Close() }()
 
 	for rows.Next() {
 		var cid int
@@ -20,6 +19,7 @@ func MigrateExternalRefColumn(db *sql.DB) error {
 		var dflt *string
 		err := rows.Scan(&cid, &name, &typ, &notnull, &dflt, &pk)
 		if err != nil {
+			rows.Close()
 			return fmt.Errorf("failed to scan column info: %w", err)
 		}
 		if name == "external_ref" {
@@ -29,9 +29,13 @@ func MigrateExternalRefColumn(db *sql.DB) error {
 	}
 
 	if err := rows.Err(); err != nil {
+		rows.Close()
 		return fmt.Errorf("error reading column info: %w", err)
 	}
 
+	// Close rows before executing any statements to avoid deadlock with MaxOpenConns(1)
+	rows.Close()
+
 	if !columnExists {
 		_, err := db.Exec(`ALTER TABLE issues ADD COLUMN external_ref TEXT`)
 		if err != nil {

internal/storage/sqlite/schema.go

@@ -47,6 +47,7 @@ CREATE TABLE IF NOT EXISTS dependencies (
 CREATE INDEX IF NOT EXISTS idx_dependencies_issue ON dependencies(issue_id);
 CREATE INDEX IF NOT EXISTS idx_dependencies_depends_on ON dependencies(depends_on_id);
 CREATE INDEX IF NOT EXISTS idx_dependencies_depends_on_type ON dependencies(depends_on_id, type);
+CREATE INDEX IF NOT EXISTS idx_dependencies_depends_on_type_issue ON dependencies(depends_on_id, type, issue_id);
 
 -- Labels table
 CREATE TABLE IF NOT EXISTS labels (

internal/storage/sqlite/sqlite.go

@@ -14,8 +14,10 @@ import (
 
 	// Import SQLite driver
 	"github.com/steveyegge/beads/internal/types"
+	sqlite3 "github.com/ncruces/go-sqlite3"
 	_ "github.com/ncruces/go-sqlite3/driver"
 	_ "github.com/ncruces/go-sqlite3/embed"
+	"github.com/tetratelabs/wazero"
 )
 
 // SQLiteStorage implements the Storage interface using SQLite
@@ -25,6 +27,53 @@ type SQLiteStorage struct {
 	closed atomic.Bool // Tracks whether Close() has been called
 }
 
+// setupWASMCache configures WASM compilation caching to reduce SQLite startup time.
+// Returns the cache directory path (empty string if using in-memory cache).
+//
+// Cache behavior:
+//   - Location: ~/.cache/beads/wasm/ (platform-specific via os.UserCacheDir)
+//   - Version management: wazero automatically keys cache by its version
+//   - Cleanup: Old versions remain harmless (~5-10MB each); manual cleanup if needed
+//   - Fallback: Uses in-memory cache if filesystem cache creation fails
+//
+// Performance impact:
+//   - First run: ~220ms (compile + cache)
+//   - Subsequent runs: ~20ms (load from cache)
+func setupWASMCache() string {
+	cacheDir := ""
+	if userCache, err := os.UserCacheDir(); err == nil {
+		cacheDir = filepath.Join(userCache, "beads", "wasm")
+	}
+
+	var cache wazero.CompilationCache
+	if cacheDir != "" {
+		// Try file-system cache first (persistent across runs)
+		if c, err := wazero.NewCompilationCacheWithDir(cacheDir); err == nil {
+			cache = c
+			// Optional: log cache location for debugging
+			// fmt.Fprintf(os.Stderr, "WASM cache: %s\n", cacheDir)
+		}
+	}
+
+	// Fallback to in-memory cache if dir creation failed
+	if cache == nil {
+		cache = wazero.NewCompilationCache()
+		cacheDir = "" // Indicate in-memory fallback
+		// Optional: log fallback for debugging
+		// fmt.Fprintln(os.Stderr, "WASM cache: in-memory only")
+	}
+
+	// Configure go-sqlite3's wazero runtime to use the cache
+	sqlite3.RuntimeConfig = wazero.NewRuntimeConfig().WithCompilationCache(cache)
+
+	return cacheDir
+}
+
+func init() {
+	// Setup WASM compilation cache to avoid 220ms JIT compilation overhead on every process start
+	_ = setupWASMCache()
+}
+
 // New creates a new SQLite storage backend
 func New(path string) (*SQLiteStorage, error) {
 	// Build connection string with proper URI syntax
@@ -56,11 +105,14 @@ func New(path string) (*SQLiteStorage, error) {
 		return nil, fmt.Errorf("failed to open database: %w", err)
 	}
 
-	// For :memory: databases, force single connection to ensure cache sharing works properly.
+	// For all in-memory databases (including file::memory:), force single connection.
-	// SQLite's shared cache mode for in-memory databases only works reliably with one connection.
+	// SQLite's in-memory databases are isolated per connection by default.
-	// Without this, different connections in the pool can't see each other's writes (bd-b121).
+	// Without this, different connections in the pool can't see each other's writes (bd-b121, bd-yvlc).
-	if path == ":memory:" {
+	isInMemory := path == ":memory:" ||
+		(strings.HasPrefix(path, "file:") && strings.Contains(path, "mode=memory"))
+	if isInMemory {
 		db.SetMaxOpenConns(1)
+		db.SetMaxIdleConns(1)
 	}
 
 	// Test connection

internal/storage/sqlite/sqlite_bench_test.go

@@ -0,0 +1,145 @@
+//go:build bench
+
+package sqlite
+
+import (
+	"context"
+	"testing"
+
+	"github.com/steveyegge/beads/internal/types"
+)
+
+// Benchmark size rationale:
+// We only benchmark Large (10K) and XLarge (20K) databases because:
+// - Small databases (<1K issues) perform acceptably without optimization
+// - Performance issues only manifest at scale (10K+ issues)
+// - Smaller benchmarks add code weight without providing optimization insights
+// - Target users manage repos with thousands of issues, not hundreds
+
+// runBenchmark sets up a benchmark with consistent configuration and runs the provided test function.
+// It handles store setup/cleanup, timer management, and allocation reporting uniformly across all benchmarks.
+func runBenchmark(b *testing.B, setupFunc func(*testing.B) (*SQLiteStorage, func()), testFunc func(*SQLiteStorage, context.Context) error) {
+	b.Helper()
+
+	store, cleanup := setupFunc(b)
+	defer cleanup()
+
+	ctx := context.Background()
+
+	b.ResetTimer()
+	b.ReportAllocs()
+
+	for i := 0; i < b.N; i++ {
+		if err := testFunc(store, ctx); err != nil {
+			b.Fatalf("benchmark failed: %v", err)
+		}
+	}
+}
+
+// BenchmarkGetReadyWork_Large benchmarks GetReadyWork on 10K issue database
+func BenchmarkGetReadyWork_Large(b *testing.B) {
+	runBenchmark(b, setupLargeBenchDB, func(store *SQLiteStorage, ctx context.Context) error {
+		_, err := store.GetReadyWork(ctx, types.WorkFilter{})
+		return err
+	})
+}
+
+// BenchmarkGetReadyWork_XLarge benchmarks GetReadyWork on 20K issue database
+func BenchmarkGetReadyWork_XLarge(b *testing.B) {
+	runBenchmark(b, setupXLargeBenchDB, func(store *SQLiteStorage, ctx context.Context) error {
+		_, err := store.GetReadyWork(ctx, types.WorkFilter{})
+		return err
+	})
+}
+
+// BenchmarkSearchIssues_Large_NoFilter benchmarks searching all open issues
+func BenchmarkSearchIssues_Large_NoFilter(b *testing.B) {
+	openStatus := types.StatusOpen
+	filter := types.IssueFilter{
+		Status: &openStatus,
+	}
+
+	runBenchmark(b, setupLargeBenchDB, func(store *SQLiteStorage, ctx context.Context) error {
+		_, err := store.SearchIssues(ctx, "", filter)
+		return err
+	})
+}
+
+// BenchmarkSearchIssues_Large_ComplexFilter benchmarks complex filtered search
+func BenchmarkSearchIssues_Large_ComplexFilter(b *testing.B) {
+	openStatus := types.StatusOpen
+	filter := types.IssueFilter{
+		Status:      &openStatus,
+		PriorityMin: intPtr(0),
+		PriorityMax: intPtr(2),
+	}
+
+	runBenchmark(b, setupLargeBenchDB, func(store *SQLiteStorage, ctx context.Context) error {
+		_, err := store.SearchIssues(ctx, "", filter)
+		return err
+	})
+}
+
+// BenchmarkCreateIssue_Large benchmarks issue creation in large database
+func BenchmarkCreateIssue_Large(b *testing.B) {
+	runBenchmark(b, setupLargeBenchDB, func(store *SQLiteStorage, ctx context.Context) error {
+		issue := &types.Issue{
+			Title:       "Benchmark issue",
+			Description: "Test description",
+			Status:      types.StatusOpen,
+			Priority:    2,
+			IssueType:   types.TypeTask,
+		}
+		return store.CreateIssue(ctx, issue, "bench")
+	})
+}
+
+// BenchmarkUpdateIssue_Large benchmarks issue updates in large database
+func BenchmarkUpdateIssue_Large(b *testing.B) {
+	// Setup phase: get an issue to update (not timed)
+	store, cleanup := setupLargeBenchDB(b)
+	defer cleanup()
+	ctx := context.Background()
+
+	openStatus := types.StatusOpen
+	issues, err := store.SearchIssues(ctx, "", types.IssueFilter{
+		Status: &openStatus,
+	})
+	if err != nil || len(issues) == 0 {
+		b.Fatalf("Failed to get issues for update test: %v", err)
+	}
+	targetID := issues[0].ID
+
+	// Benchmark phase: measure update operations
+	b.ResetTimer()
+	b.ReportAllocs()
+
+	for i := 0; i < b.N; i++ {
+		updates := map[string]interface{}{
+			"status": types.StatusInProgress,
+		}
+
+		if err := store.UpdateIssue(ctx, targetID, updates, "bench"); err != nil {
+			b.Fatalf("UpdateIssue failed: %v", err)
+		}
+
+		// reset back to open for next iteration
+		updates["status"] = types.StatusOpen
+		if err := store.UpdateIssue(ctx, targetID, updates, "bench"); err != nil {
+			b.Fatalf("UpdateIssue failed: %v", err)
+		}
+	}
+}
+
+// BenchmarkGetReadyWork_FromJSONL benchmarks ready work on JSONL-imported database
+func BenchmarkGetReadyWork_FromJSONL(b *testing.B) {
+	runBenchmark(b, setupLargeFromJSONL, func(store *SQLiteStorage, ctx context.Context) error {
+		_, err := store.GetReadyWork(ctx, types.WorkFilter{})
+		return err
+	})
+}
+
+// Helper function
+func intPtr(i int) *int {
+	return &i
+}

internal/testutil/fixtures/fixtures.go

@@ -0,0 +1,541 @@
+// Package fixtures provides realistic test data generation for benchmarks and tests.
+package fixtures
+
+import (
+	"context"
+	"encoding/json"
+	"fmt"
+	"math/rand"
+	"os"
+	"path/filepath"
+	"strings"
+	"time"
+
+	"github.com/steveyegge/beads/internal/storage"
+	"github.com/steveyegge/beads/internal/types"
+)
+
+// labels used across all fixtures
+var commonLabels = []string{
+	"backend",
+	"frontend",
+	"urgent",
+	"tech-debt",
+	"documentation",
+	"performance",
+	"security",
+	"ux",
+	"api",
+	"database",
+}
+
+// assignees used across all fixtures
+var commonAssignees = []string{
+	"alice",
+	"bob",
+	"charlie",
+	"diana",
+	"eve",
+	"frank",
+}
+
+// epic titles for realistic data
+var epicTitles = []string{
+	"User Authentication System",
+	"Payment Processing Integration",
+	"Mobile App Redesign",
+	"Performance Optimization",
+	"API v2 Migration",
+	"Search Functionality Enhancement",
+	"Analytics Dashboard",
+	"Multi-tenant Support",
+	"Notification System",
+	"Data Export Feature",
+}
+
+// feature titles (under epics)
+var featureTitles = []string{
+	"OAuth2 Integration",
+	"Password Reset Flow",
+	"Two-Factor Authentication",
+	"Session Management",
+	"API Endpoints",
+	"Database Schema",
+	"UI Components",
+	"Background Jobs",
+	"Error Handling",
+	"Testing Infrastructure",
+}
+
+// task titles (under features)
+var taskTitles = []string{
+	"Implement login endpoint",
+	"Add validation logic",
+	"Write unit tests",
+	"Update documentation",
+	"Fix memory leak",
+	"Optimize query performance",
+	"Add error logging",
+	"Refactor helper functions",
+	"Update database migrations",
+	"Configure deployment",
+}
+
+// Fixture size rationale:
+// We only provide Large (10K) and XLarge (20K) fixtures because:
+// - Performance characteristics only emerge at scale (10K+ issues)
+// - Smaller fixtures don't provide meaningful optimization insights
+// - Code weight matters; we avoid unused complexity
+// - Target use case: repositories with thousands of issues
+
+// DataConfig controls the distribution and characteristics of generated test data
+type DataConfig struct {
+	TotalIssues      int     // total number of issues to generate
+	EpicRatio        float64 // percentage of issues that are epics (e.g., 0.1 for 10%)
+	FeatureRatio     float64 // percentage of issues that are features (e.g., 0.3 for 30%)
+	OpenRatio        float64 // percentage of issues that are open (e.g., 0.5 for 50%)
+	CrossLinkRatio   float64 // percentage of tasks with cross-epic blocking dependencies (e.g., 0.2 for 20%)
+	MaxEpicAgeDays   int     // maximum age in days for epics (e.g., 180)
+	MaxFeatureAgeDays int    // maximum age in days for features (e.g., 150)
+	MaxTaskAgeDays   int     // maximum age in days for tasks (e.g., 120)
+	MaxClosedAgeDays int     // maximum days since closure (e.g., 30)
+	RandSeed         int64   // random seed for reproducibility
+}
+
+// DefaultLargeConfig returns configuration for 10K issue dataset
+func DefaultLargeConfig() DataConfig {
+	return DataConfig{
+		TotalIssues:      10000,
+		EpicRatio:        0.1,
+		FeatureRatio:     0.3,
+		OpenRatio:        0.5,
+		CrossLinkRatio:   0.2,
+		MaxEpicAgeDays:   180,
+		MaxFeatureAgeDays: 150,
+		MaxTaskAgeDays:   120,
+		MaxClosedAgeDays: 30,
+		RandSeed:         42,
+	}
+}
+
+// DefaultXLargeConfig returns configuration for 20K issue dataset
+func DefaultXLargeConfig() DataConfig {
+	return DataConfig{
+		TotalIssues:      20000,
+		EpicRatio:        0.1,
+		FeatureRatio:     0.3,
+		OpenRatio:        0.5,
+		CrossLinkRatio:   0.2,
+		MaxEpicAgeDays:   180,
+		MaxFeatureAgeDays: 150,
+		MaxTaskAgeDays:   120,
+		MaxClosedAgeDays: 30,
+		RandSeed:         43,
+	}
+}
+
+// LargeSQLite creates a 10K issue database with realistic patterns
+func LargeSQLite(ctx context.Context, store storage.Storage) error {
+	cfg := DefaultLargeConfig()
+	return generateIssuesWithConfig(ctx, store, cfg)
+}
+
+// XLargeSQLite creates a 20K issue database with realistic patterns
+func XLargeSQLite(ctx context.Context, store storage.Storage) error {
+	cfg := DefaultXLargeConfig()
+	return generateIssuesWithConfig(ctx, store, cfg)
+}
+
+// LargeFromJSONL creates a 10K issue database by exporting to JSONL and reimporting
+func LargeFromJSONL(ctx context.Context, store storage.Storage, tempDir string) error {
+	cfg := DefaultLargeConfig()
+	cfg.RandSeed = 44 // different seed for JSONL path
+	return generateFromJSONL(ctx, store, tempDir, cfg)
+}
+
+// XLargeFromJSONL creates a 20K issue database by exporting to JSONL and reimporting
+func XLargeFromJSONL(ctx context.Context, store storage.Storage, tempDir string) error {
+	cfg := DefaultXLargeConfig()
+	cfg.RandSeed = 45 // different seed for JSONL path
+	return generateFromJSONL(ctx, store, tempDir, cfg)
+}
+
+// generateIssuesWithConfig creates issues with realistic epic hierarchies and cross-links using provided configuration
+func generateIssuesWithConfig(ctx context.Context, store storage.Storage, cfg DataConfig) error {
+	rng := rand.New(rand.NewSource(cfg.RandSeed))
+
+	// Calculate breakdown using configuration ratios
+	numEpics := int(float64(cfg.TotalIssues) * cfg.EpicRatio)
+	numFeatures := int(float64(cfg.TotalIssues) * cfg.FeatureRatio)
+	numTasks := cfg.TotalIssues - numEpics - numFeatures
+
+	// Track created issues for cross-linking
+	var allIssues []*types.Issue
+	epicIssues := make([]*types.Issue, 0, numEpics)
+	featureIssues := make([]*types.Issue, 0, numFeatures)
+	taskIssues := make([]*types.Issue, 0, numTasks)
+
+	// Progress tracking
+	createdIssues := 0
+	lastPctLogged := -1
+
+	logProgress := func() {
+		pct := (createdIssues * 100) / cfg.TotalIssues
+		if pct >= lastPctLogged+10 {
+			fmt.Printf("  Progress: %d%% (%d/%d issues created)\n", pct, createdIssues, cfg.TotalIssues)
+			lastPctLogged = pct
+		}
+	}
+
+	// Create epics
+	for i := 0; i < numEpics; i++ {
+		issue := &types.Issue{
+			Title:       fmt.Sprintf("%s (Epic %d)", epicTitles[i%len(epicTitles)], i),
+			Description: fmt.Sprintf("Epic for %s", epicTitles[i%len(epicTitles)]),
+			Status:      randomStatus(rng, cfg.OpenRatio),
+			Priority:    randomPriority(rng),
+			IssueType:   types.TypeEpic,
+			Assignee:    commonAssignees[rng.Intn(len(commonAssignees))],
+			CreatedAt:   randomTime(rng, cfg.MaxEpicAgeDays),
+			UpdatedAt:   time.Now(),
+		}
+
+		if issue.Status == types.StatusClosed {
+			closedAt := randomTime(rng, cfg.MaxClosedAgeDays)
+			issue.ClosedAt = &closedAt
+		}
+
+		if err := store.CreateIssue(ctx, issue, "fixture"); err != nil {
+			return fmt.Errorf("failed to create epic: %w", err)
+		}
+
+		// Add labels to epics
+		for j := 0; j < rng.Intn(3)+1; j++ {
+			label := commonLabels[rng.Intn(len(commonLabels))]
+			_ = store.AddLabel(ctx, issue.ID, label, "fixture")
+		}
+
+		epicIssues = append(epicIssues, issue)
+		allIssues = append(allIssues, issue)
+		createdIssues++
+		logProgress()
+	}
+
+	// Create features under epics
+	for i := 0; i < numFeatures; i++ {
+		parentEpic := epicIssues[i%len(epicIssues)]
+
+		issue := &types.Issue{
+			Title:       fmt.Sprintf("%s (Feature %d)", featureTitles[i%len(featureTitles)], i),
+			Description: fmt.Sprintf("Feature under %s", parentEpic.Title),
+			Status:      randomStatus(rng, cfg.OpenRatio),
+			Priority:    randomPriority(rng),
+			IssueType:   types.TypeFeature,
+			Assignee:    commonAssignees[rng.Intn(len(commonAssignees))],
+			CreatedAt:   randomTime(rng, cfg.MaxFeatureAgeDays),
+			UpdatedAt:   time.Now(),
+		}
+
+		if issue.Status == types.StatusClosed {
+			closedAt := randomTime(rng, cfg.MaxClosedAgeDays)
+			issue.ClosedAt = &closedAt
+		}
+
+		if err := store.CreateIssue(ctx, issue, "fixture"); err != nil {
+			return fmt.Errorf("failed to create feature: %w", err)
+		}
+
+		// Add parent-child dependency to epic
+		dep := &types.Dependency{
+			IssueID:     issue.ID,
+			DependsOnID: parentEpic.ID,
+			Type:        types.DepParentChild,
+			CreatedAt:   time.Now(),
+			CreatedBy:   "fixture",
+		}
+		if err := store.AddDependency(ctx, dep, "fixture"); err != nil {
+			return fmt.Errorf("failed to add feature-epic dependency: %w", err)
+		}
+
+		// Add labels
+		for j := 0; j < rng.Intn(3)+1; j++ {
+			label := commonLabels[rng.Intn(len(commonLabels))]
+			_ = store.AddLabel(ctx, issue.ID, label, "fixture")
+		}
+
+		featureIssues = append(featureIssues, issue)
+		allIssues = append(allIssues, issue)
+		createdIssues++
+		logProgress()
+	}
+
+	// Create tasks under features
+	for i := 0; i < numTasks; i++ {
+		parentFeature := featureIssues[i%len(featureIssues)]
+
+		issue := &types.Issue{
+			Title:       fmt.Sprintf("%s (Task %d)", taskTitles[i%len(taskTitles)], i),
+			Description: fmt.Sprintf("Task under %s", parentFeature.Title),
+			Status:      randomStatus(rng, cfg.OpenRatio),
+			Priority:    randomPriority(rng),
+			IssueType:   types.TypeTask,
+			Assignee:    commonAssignees[rng.Intn(len(commonAssignees))],
+			CreatedAt:   randomTime(rng, cfg.MaxTaskAgeDays),
+			UpdatedAt:   time.Now(),
+		}
+
+		if issue.Status == types.StatusClosed {
+			closedAt := randomTime(rng, cfg.MaxClosedAgeDays)
+			issue.ClosedAt = &closedAt
+		}
+
+		if err := store.CreateIssue(ctx, issue, "fixture"); err != nil {
+			return fmt.Errorf("failed to create task: %w", err)
+		}
+
+		// Add parent-child dependency to feature
+		dep := &types.Dependency{
+			IssueID:     issue.ID,
+			DependsOnID: parentFeature.ID,
+			Type:        types.DepParentChild,
+			CreatedAt:   time.Now(),
+			CreatedBy:   "fixture",
+		}
+		if err := store.AddDependency(ctx, dep, "fixture"); err != nil {
+			return fmt.Errorf("failed to add task-feature dependency: %w", err)
+		}
+
+		// Add labels
+		for j := 0; j < rng.Intn(2)+1; j++ {
+			label := commonLabels[rng.Intn(len(commonLabels))]
+			_ = store.AddLabel(ctx, issue.ID, label, "fixture")
+		}
+
+		taskIssues = append(taskIssues, issue)
+		allIssues = append(allIssues, issue)
+		createdIssues++
+		logProgress()
+	}
+
+	fmt.Printf("  Progress: 100%% (%d/%d issues created) - Complete!\n", cfg.TotalIssues, cfg.TotalIssues)
+
+	// Add cross-links between tasks across epics using configured ratio
+	numCrossLinks := int(float64(numTasks) * cfg.CrossLinkRatio)
+	for i := 0; i < numCrossLinks; i++ {
+		fromTask := taskIssues[rng.Intn(len(taskIssues))]
+		toTask := taskIssues[rng.Intn(len(taskIssues))]
+
+		// Avoid self-dependencies
+		if fromTask.ID == toTask.ID {
+			continue
+		}
+
+		dep := &types.Dependency{
+			IssueID:     fromTask.ID,
+			DependsOnID: toTask.ID,
+			Type:        types.DepBlocks,
+			CreatedAt:   time.Now(),
+			CreatedBy:   "fixture",
+		}
+
+		// Ignore cycle errors for cross-links (they're expected)
+		_ = store.AddDependency(ctx, dep, "fixture")
+	}
+
+	return nil
+}
+
+// generateFromJSONL creates issues, exports to JSONL, clears DB, and reimports
+func generateFromJSONL(ctx context.Context, store storage.Storage, tempDir string, cfg DataConfig) error {
+	// First generate issues normally
+	if err := generateIssuesWithConfig(ctx, store, cfg); err != nil {
+		return fmt.Errorf("failed to generate issues: %w", err)
+	}
+
+	// Export to JSONL
+	jsonlPath := filepath.Join(tempDir, "issues.jsonl")
+	if err := exportToJSONL(ctx, store, jsonlPath); err != nil {
+		return fmt.Errorf("failed to export to JSONL: %w", err)
+	}
+
+	// Clear all issues (we'll reimport them)
+	allIssues, err := store.SearchIssues(ctx, "", types.IssueFilter{})
+	if err != nil {
+		return fmt.Errorf("failed to get all issues: %w", err)
+	}
+
+	for _, issue := range allIssues {
+		if err := store.DeleteIssue(ctx, issue.ID); err != nil {
+			return fmt.Errorf("failed to delete issue %s: %w", issue.ID, err)
+		}
+	}
+
+	// Import from JSONL
+	if err := importFromJSONL(ctx, store, jsonlPath); err != nil {
+		return fmt.Errorf("failed to import from JSONL: %w", err)
+	}
+
+	return nil
+}
+
+// exportToJSONL exports all issues to a JSONL file
+func exportToJSONL(ctx context.Context, store storage.Storage, path string) error {
+	// Get all issues
+	allIssues, err := store.SearchIssues(ctx, "", types.IssueFilter{})
+	if err != nil {
+		return fmt.Errorf("failed to query issues: %w", err)
+	}
+
+	// Populate dependencies and labels for each issue
+	allDeps, err := store.GetAllDependencyRecords(ctx)
+	if err != nil {
+		return fmt.Errorf("failed to get dependencies: %w", err)
+	}
+
+	for _, issue := range allIssues {
+		issue.Dependencies = allDeps[issue.ID]
+
+		labels, err := store.GetLabels(ctx, issue.ID)
+		if err != nil {
+			return fmt.Errorf("failed to get labels for %s: %w", issue.ID, err)
+		}
+		issue.Labels = labels
+	}
+
+	// Write to JSONL file
+	f, err := os.Create(path)
+	if err != nil {
+		return fmt.Errorf("failed to create JSONL file: %w", err)
+	}
+	defer f.Close()
+
+	encoder := json.NewEncoder(f)
+	for _, issue := range allIssues {
+		if err := encoder.Encode(issue); err != nil {
+			return fmt.Errorf("failed to encode issue: %w", err)
+		}
+	}
+
+	return nil
+}
+
+// importFromJSONL imports issues from a JSONL file
+func importFromJSONL(ctx context.Context, store storage.Storage, path string) error {
+	// Read JSONL file
+	data, err := os.ReadFile(path)
+	if err != nil {
+		return fmt.Errorf("failed to read JSONL file: %w", err)
+	}
+
+	// Parse issues
+	var issues []*types.Issue
+	lines := string(data)
+	for i, line := range splitLines(lines) {
+		if len(line) == 0 {
+			continue
+		}
+
+		var issue types.Issue
+		if err := json.Unmarshal([]byte(line), &issue); err != nil {
+			return fmt.Errorf("failed to parse issue at line %d: %w", i+1, err)
+		}
+
+		issues = append(issues, &issue)
+	}
+
+	// Import issues directly using storage interface
+	// Step 1: Create all issues first (without dependencies/labels)
+	type savedMetadata struct {
+		deps   []*types.Dependency
+		labels []string
+	}
+	metadata := make(map[string]savedMetadata)
+
+	for _, issue := range issues {
+		// Save dependencies and labels for later
+		metadata[issue.ID] = savedMetadata{
+			deps:   issue.Dependencies,
+			labels: issue.Labels,
+		}
+		issue.Dependencies = nil
+		issue.Labels = nil
+
+		if err := store.CreateIssue(ctx, issue, "fixture"); err != nil {
+			// Ignore duplicate errors
+			if !strings.Contains(err.Error(), "UNIQUE constraint failed") {
+				return fmt.Errorf("failed to create issue %s: %w", issue.ID, err)
+			}
+		}
+	}
+
+	// Step 2: Add all dependencies (now that all issues exist)
+	for issueID, meta := range metadata {
+		for _, dep := range meta.deps {
+			if err := store.AddDependency(ctx, dep, "fixture"); err != nil {
+				// Ignore duplicate and cycle errors
+				if !strings.Contains(err.Error(), "already exists") &&
+					!strings.Contains(err.Error(), "cycle") {
+					return fmt.Errorf("failed to add dependency for %s: %w", issueID, err)
+				}
+			}
+		}
+
+		// Add labels
+		for _, label := range meta.labels {
+			_ = store.AddLabel(ctx, issueID, label, "fixture")
+		}
+	}
+
+	return nil
+}
+
+// splitLines splits a string by newlines
+func splitLines(s string) []string {
+	var lines []string
+	start := 0
+	for i := 0; i < len(s); i++ {
+		if s[i] == '\n' {
+			lines = append(lines, s[start:i])
+			start = i + 1
+		}
+	}
+	if start < len(s) {
+		lines = append(lines, s[start:])
+	}
+	return lines
+}
+
+// randomStatus returns a random status with given open ratio
+func randomStatus(rng *rand.Rand, openRatio float64) types.Status {
+	r := rng.Float64()
+	if r < openRatio {
+		// Open statuses: open, in_progress, blocked
+		statuses := []types.Status{types.StatusOpen, types.StatusInProgress, types.StatusBlocked}
+		return statuses[rng.Intn(len(statuses))]
+	}
+	return types.StatusClosed
+}
+
+// randomPriority returns a random priority with realistic distribution
+// P0: 5%, P1: 15%, P2: 50%, P3: 25%, P4: 5%
+func randomPriority(rng *rand.Rand) int {
+	r := rng.Intn(100)
+	switch {
+	case r < 5:
+		return 0
+	case r < 20:
+		return 1
+	case r < 70:
+		return 2
+	case r < 95:
+		return 3
+	default:
+		return 4
+	}
+}
+
+// randomTime returns a random time up to maxDaysAgo days in the past
+func randomTime(rng *rand.Rand, maxDaysAgo int) time.Time {
+	daysAgo := rng.Intn(maxDaysAgo)
+	return time.Now().Add(-time.Duration(daysAgo) * 24 * time.Hour)
+}

internal/testutil/fixtures/fixtures_test.go

@@ -0,0 +1,128 @@
+package fixtures
+
+import (
+	"context"
+	"testing"
+
+	"github.com/steveyegge/beads/internal/storage/sqlite"
+	"github.com/steveyegge/beads/internal/types"
+)
+
+func TestLargeSQLite(t *testing.T) {
+	tmpDB := t.TempDir() + "/test.db"
+	store, err := sqlite.New(tmpDB)
+	if err != nil {
+		t.Fatalf("Failed to create storage: %v", err)
+	}
+	defer store.Close()
+
+	ctx := context.Background()
+
+	// Initialize database with prefix
+	if err := store.SetConfig(ctx, "issue_prefix", "bd-"); err != nil {
+		t.Fatalf("Failed to set issue_prefix: %v", err)
+	}
+
+	if err := LargeSQLite(ctx, store); err != nil {
+		t.Fatalf("LargeSQLite failed: %v", err)
+	}
+
+	// Verify issue count
+	allIssues, err := store.SearchIssues(ctx, "", types.IssueFilter{})
+	if err != nil {
+		t.Fatalf("Failed to search issues: %v", err)
+	}
+
+	if len(allIssues) != 10000 {
+		t.Errorf("Expected 10000 issues, got %d", len(allIssues))
+	}
+
+	// Verify we have epics, features, and tasks
+	var epics, features, tasks int
+	for _, issue := range allIssues {
+		switch issue.IssueType {
+		case types.TypeEpic:
+			epics++
+		case types.TypeFeature:
+			features++
+		case types.TypeTask:
+			tasks++
+		}
+	}
+
+	if epics == 0 || features == 0 || tasks == 0 {
+		t.Errorf("Missing issue types: epics=%d, features=%d, tasks=%d", epics, features, tasks)
+	}
+
+	t.Logf("Created %d epics, %d features, %d tasks", epics, features, tasks)
+}
+
+func TestXLargeSQLite(t *testing.T) {
+	if testing.Short() {
+		t.Skip("Skipping XLarge test in short mode")
+	}
+
+	tmpDB := t.TempDir() + "/test.db"
+	store, err := sqlite.New(tmpDB)
+	if err != nil {
+		t.Fatalf("Failed to create storage: %v", err)
+	}
+	defer store.Close()
+
+	ctx := context.Background()
+
+	// Initialize database with prefix
+	if err := store.SetConfig(ctx, "issue_prefix", "bd-"); err != nil {
+		t.Fatalf("Failed to set issue_prefix: %v", err)
+	}
+
+	if err := XLargeSQLite(ctx, store); err != nil {
+		t.Fatalf("XLargeSQLite failed: %v", err)
+	}
+
+	// Verify issue count
+	allIssues, err := store.SearchIssues(ctx, "", types.IssueFilter{})
+	if err != nil {
+		t.Fatalf("Failed to search issues: %v", err)
+	}
+
+	if len(allIssues) != 20000 {
+		t.Errorf("Expected 20000 issues, got %d", len(allIssues))
+	}
+}
+
+func TestLargeFromJSONL(t *testing.T) {
+	if testing.Short() {
+		t.Skip("Skipping JSONL test in short mode")
+	}
+
+	tmpDB := t.TempDir() + "/test.db"
+	store, err := sqlite.New(tmpDB)
+	if err != nil {
+		t.Fatalf("Failed to create storage: %v", err)
+	}
+	defer store.Close()
+
+	ctx := context.Background()
+
+	// Initialize database with prefix
+	if err := store.SetConfig(ctx, "issue_prefix", "bd-"); err != nil {
+		t.Fatalf("Failed to set issue_prefix: %v", err)
+	}
+
+	tempDir := t.TempDir()
+
+	if err := LargeFromJSONL(ctx, store, tempDir); err != nil {
+		t.Fatalf("LargeFromJSONL failed: %v", err)
+	}
+
+	// Verify issue count
+	allIssues, err := store.SearchIssues(ctx, "", types.IssueFilter{})
+	if err != nil {
+		t.Fatalf("Failed to search issues: %v", err)
+	}
+
+	if len(allIssues) != 10000 {
+		t.Errorf("Expected 10000 issues, got %d", len(allIssues))
+	}
+}

internal/utils/id_parser.go

@@ -81,14 +81,41 @@ func ResolvePartialID(ctx context.Context, store storage.Storage, input string)
 	hashPart := strings.TrimPrefix(normalizedID, prefixWithHyphen)
 
 	var matches []string
+	var exactMatch string
+	
 	for _, issue := range issues {
-		issueHash := strings.TrimPrefix(issue.ID, prefixWithHyphen)
+		// Check for exact full ID match first (case: user typed full ID with different prefix)
+		if issue.ID == input {
+			exactMatch = issue.ID
+			break
+		}
+		
+		// Extract hash from each issue, regardless of its prefix
+		// This handles cross-prefix matching (e.g., "3d0" matching "offlinebrew-3d0")
+		var issueHash string
+		if idx := strings.Index(issue.ID, "-"); idx >= 0 {
+			issueHash = issue.ID[idx+1:]
+		} else {
+			issueHash = issue.ID
+		}
+		
+		// Check for exact hash match (excluding hierarchical children)
+		if issueHash == hashPart {
+			exactMatch = issue.ID
+			// Don't break - keep searching in case there's a full ID match
+		}
+		
 		// Check if the issue hash contains the input hash as substring
 		if strings.Contains(issueHash, hashPart) {
 			matches = append(matches, issue.ID)
 		}
 	}
 	
+	// Prefer exact match over substring matches
+	if exactMatch != "" {
+		return exactMatch, nil
+	}
+	
 	if len(matches) == 0 {
 		return "", fmt.Errorf("no issue found matching %q", input)
 	}

internal/utils/id_parser_test.go

@@ -90,6 +90,21 @@ func TestResolvePartialID(t *testing.T) {
 		Priority:  1,
 		IssueType: types.TypeTask,
 	}
+	// Test hierarchical IDs - parent and child
+	parentIssue := &types.Issue{
+		ID:        "offlinebrew-3d0",
+		Title:     "Parent Epic",
+		Status:    types.StatusOpen,
+		Priority:  1,
+		IssueType: types.TypeEpic,
+	}
+	childIssue := &types.Issue{
+		ID:        "offlinebrew-3d0.1",
+		Title:     "Child Task",
+		Status:    types.StatusOpen,
+		Priority:  1,
+		IssueType: types.TypeTask,
+	}
 	
 	if err := store.CreateIssue(ctx, issue1, "test"); err != nil {
 		t.Fatal(err)
@@ -100,6 +115,12 @@ func TestResolvePartialID(t *testing.T) {
 	if err := store.CreateIssue(ctx, issue3, "test"); err != nil {
 		t.Fatal(err)
 	}
+	if err := store.CreateIssue(ctx, parentIssue, "test"); err != nil {
+		t.Fatal(err)
+	}
+	if err := store.CreateIssue(ctx, childIssue, "test"); err != nil {
+		t.Fatal(err)
+	}
 	
 	// Set config for prefix
 	if err := store.SetConfig(ctx, "issue_prefix", "bd-"); err != nil {
@@ -149,6 +170,16 @@ func TestResolvePartialID(t *testing.T) {
 			input:       "bd-1",
 			expected:    "bd-1",  // Will match exactly, not ambiguously
 		},
+		{
+			name:     "exact match parent ID with hierarchical child - gh-316",
+			input:    "offlinebrew-3d0",
+			expected: "offlinebrew-3d0",  // Should match exactly, not be ambiguous with offlinebrew-3d0.1
+		},
+		{
+			name:     "exact match parent without prefix - gh-316",
+			input:    "3d0",
+			expected: "offlinebrew-3d0",  // Should still prefer exact hash match
+		},
 	}
 
 	for _, tt := range tests {