Performance Improvements (#319)

* feat: add performance testing framework foundation

Implements foundation for comprehensive performance testing and user
diagnostics for beads databases at 10K-20K scale.

Components added:
- Fixture generator (internal/testutil/fixtures/) for realistic test data
  * LargeSQLite/XLargeSQLite: 10K/20K issues with epic hierarchies
  * LargeFromJSONL/XLargeFromJSONL: test JSONL import path
  * Realistic cross-linked dependencies, labels, assignees
  * Reproducible with seeded RNG

- User diagnostics (bd doctor --perf) for field performance data
  * Collects platform info (OS, arch, Go/SQLite versions)
  * Measures key operation timings (ready, list, show, search)
  * Generates CPU profiles for bug reports
  * Clean separation in cmd/bd/doctor/perf.go

Test data characteristics:
- 10% epics, 30% features, 60% tasks
- 4-level hierarchies (Epic → Feature → Task → Subtask)
- 20% cross-epic blocking dependencies
- Realistic status/priority/label distributions

Supports bd-l954 (Performance Testing Framework epic)
Closes bd-6ed8, bd-q59i

* perf: optimize GetReadyWork with compound index (20x speedup)

Add compound index on dependencies(depends_on_id, type, issue_id) to
eliminate performance bottleneck in GetReadyWork recursive CTE query.

Performance improvements (10K issue database):
- GetReadyWork: 752ms → 36.6ms (20.5x faster)
- Target: <50ms ✓ ACHIEVED
- 20K database: ~1500ms → 79.4ms (19x faster)

Benchmark infrastructure enhancements:
- Add dataset caching in /tmp/beads-bench-cache/ to avoid regenerating
  10K-20K issues on every benchmark run (first run: ~2min, subsequent: <5s)
- Add progress logging during fixture generation (shows 10%, 20%... completion)
- Add database size logging (17.5 MB for 10K, 35.1 MB for 20K)
- Document rationale for only benchmarking large datasets (>10K issues)
- Add CPU/trace profiling with --profile flag for performance debugging

Schema changes:
- internal/storage/sqlite/schema.go: Add idx_dependencies_depends_on_type_issue

New files:
- internal/storage/sqlite/bench_helpers_test.go: Reusable benchmark setup with caching
- internal/storage/sqlite/sqlite_bench_test.go: Comprehensive benchmarks for critical operations
- Makefile: Convenient benchmark execution (make bench-quick, make bench)

Related:
- Resolves bd-5qim (optimize GetReadyWork performance)
- Builds on bd-6ed8 (fixture generator), bd-q59i (bd doctor --perf)

* perf: add WASM compilation cache to eliminate cold-start overhead

Configure wazero compilation cache for ncruces/go-sqlite3 to avoid
~220ms JIT compilation on every process start.

Cache configuration:
- Location: ~/.cache/beads/wasm/ (platform-specific via os.UserCacheDir)
- Automatic version management: wazero keys entries by its version
- Fallback: in-memory cache if directory creation fails
- No cleanup needed: old versions are harmless (~5-10MB each)

Performance impact:
- First run: ~220ms (populate cache)
- Subsequent runs: ~20ms (load from cache)
- Savings: ~200ms per cold start

Cache invalidation:
- Automatic when wazero version changes (upgrades use new cache dir)
- Manual cleanup: rm -rf ~/.cache/beads/wasm/ (safe to delete anytime)

This complements daemon mode:
- Daemon mode: eliminates startup cost by keeping process alive
- WASM cache: reduces startup cost for one-off commands or daemon restarts

Changes:
- internal/storage/sqlite/sqlite.go: Add init() with cache setup

* refactor: improve maintainability of performance testing code

Extract common patterns and eliminate duplication across benchmarks, fixture generation, and performance diagnostics. Replace magic numbers with explicit configuration to improve readability and make it easier to tune test parameters.

* docs: clarify profiling behavior and add missing documentation

Add explanatory comments for profiling setup to clarify why --profile
forces direct mode (captures actual database operations instead of RPC
overhead) and document the stopCPUProfile function's role in flushing
profile data to disk. Also fix gosec G104 linter warning by explicitly
ignoring Close() error during cleanup.

* fix: prevent bench-quick from running indefinitely

Added //go:build bench tags and skipped timeout-prone benchmarks to
prevent make bench-quick from running for hours.

Changes:
- Add //go:build bench tag to cycle_bench_test.go and compact_bench_test.go
- Skip Dense graph benchmarks (documented to timeout >120s)
- Fix compact benchmark prefix: bd- → bd (validation expects prefix without trailing dash)

Before: make bench-quick ran for 3.5+ hours (12,699s) before manual interrupt
After: make bench-quick completes in ~25 seconds

The Dense graph benchmarks are known to timeout and represent rare edge
cases that don't need optimization for typical workflows.

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"