feat(daemon): unify auto-sync config for simpler agent workflows (#904)

* feat(daemon): unify auto-sync config for simpler agent workflows

## Problem

Agents running `bd sync` at session end caused delays in the Claude Code
"event loop", slowing development. The daemon was already auto-exporting
DB→JSONL instantly, but auto-commit and auto-push weren't enabled by
default when sync-branch was configured - requiring manual `bd sync`.

Additionally, having three separate config options (auto-commit, auto-push,
auto-pull) was confusing and could get out of sync.

## Solution

Simplify to two intuitive sync modes:

1. **Read/Write Mode** (`daemon.auto-sync: true` or `BEADS_AUTO_SYNC=true`)
   - Enables auto-commit + auto-push + auto-pull
   - Full bidirectional sync - eliminates need for manual `bd sync`
   - Default when sync-branch is configured

2. **Read-Only Mode** (`daemon.auto-pull: true` or `BEADS_AUTO_PULL=true`)
   - Only receives updates from team
   - Does NOT auto-publish changes
   - Useful for experimental work or manual review before sharing

## Benefits

- **Faster agent workflows**: No more `bd sync` delays at session end
- **Simpler config**: Two modes instead of three separate toggles
- **Backward compatible**: Legacy auto_commit/auto_push settings still work
  (treated as auto-sync=true)
- **Adaptive `bd prime`**: Session close protocol adapts when daemon is
  auto-syncing (shows simplified 4-step git workflow, no `bd sync`)
- **Doctor warnings**: `bd doctor` warns about deprecated legacy config

## Changes

- cmd/bd/daemon.go: Add loadDaemonAutoSettings() with unified config logic
- cmd/bd/doctor.go: Add CheckLegacyDaemonConfig call
- cmd/bd/doctor/daemon.go: Add CheckDaemonAutoSync, CheckLegacyDaemonConfig
- cmd/bd/init_team.go: Use daemon.auto-sync in team wizard
- cmd/bd/prime.go: Detect daemon auto-sync, adapt session close protocol
- cmd/bd/prime_test.go: Add stubIsDaemonAutoSyncing for testing

* docs: add comprehensive daemon technical analysis

Add daemon-summary.md documenting the beads daemon architecture,
memory analysis (explaining the 30-35MB footprint), platform support
comparison, historical problems and fixes, and architectural guidance
for other projects implementing similar daemon patterns.

Key sections:
- Architecture deep dive with component diagrams
- Memory breakdown (SQLite WASM runtime is the main contributor)
- Platform support matrix (macOS/Linux full, Windows partial)
- Historical bugs and their fixes with reusable patterns
- Analysis of daemon usefulness without database (verdict: low value)
- Expert-reviewed improvement proposals (3 recommended, 3 skipped)
- Technical design patterns for other implementations

* feat: add cross-platform CI matrix and dual-mode test framework

Cross-Platform CI:
- Add Windows, macOS, Linux matrix to catch platform-specific bugs
- Linux: full tests with race detector and coverage
- macOS: full tests with race detector
- Windows: full tests without race detector (performance)
- Catches bugs like GH#880 (macOS path casing) and GH#387 (Windows daemon)

Dual-Mode Test Framework (cmd/bd/dual_mode_test.go):
- Runs tests in both direct mode and daemon mode
- Prevents recurring bug pattern (GH#719, GH#751, bd-fu83)
- Provides DualModeTestEnv with helper methods for common operations
- Includes 5 example tests demonstrating the pattern

Documentation:
- Add dual-mode testing section to CONTRIBUTING.md
- Document RunDualModeTest API and available helpers

Test Fixes:
- Fix sync_local_only_test.go gitPull/gitPush calls
- Add gate_no_daemon_test.go for beads-70c4 investigation

* fix(test): isolate TestFindBeadsDir tests with BEADS_DIR env var

The tests were finding the real project's .beads directory instead of
the temp directory because FindBeadsDir() walks up the directory tree.
Using BEADS_DIR env var provides proper test isolation.

* fix(test): stop daemon before running test suite guard

The test suite guard checks that tests don't modify the real repo's .beads
directory. However, a background daemon running auto-sync would touch
issues.jsonl during test execution, causing false positives.

Changes:
- Set BEADS_NO_DAEMON=1 to prevent daemon auto-start from tests
- Stop any running daemon for the repo before taking the "before" snapshot
- Uses exec to call `bd daemon --stop` to avoid import cycle issues

* chore: revert .beads/issues.jsonl to upstream/main

Per CONTRIBUTING.md, .beads/issues.jsonl should not be modified in PRs.

internal/storage/sqlite/gate_no_daemon_test.go

@@ -0,0 +1,97 @@
+package sqlite
+
+import (
+	"context"
+	"testing"
+	"time"
+
+	"github.com/steveyegge/beads/internal/types"
+)
+
+// TestGateFieldsPreservedAcrossConnections reproduces beads-70c4:
+// Gate await fields should not be cleared when a new database connection
+// is opened (simulating --no-daemon CLI access).
+func TestGateFieldsPreservedAcrossConnections(t *testing.T) {
+	// Use a temporary file database (not :memory:) to simulate real-world scenario
+	dbPath := t.TempDir() + "/beads.db"
+
+	ctx := context.Background()
+
+	// Step 1: Create a database and add a gate with await fields
+	// (simulating daemon creating a gate)
+	store1, err := New(ctx, dbPath)
+	if err != nil {
+		t.Fatalf("failed to create first store: %v", err)
+	}
+
+	// Initialize the database with a prefix
+	if err := store1.SetConfig(ctx, "issue_prefix", "beads"); err != nil {
+		t.Fatalf("failed to set issue_prefix: %v", err)
+	}
+
+	gate := &types.Issue{
+		ID:        "beads-test1",
+		Title:     "Test Gate",
+		Status:    types.StatusOpen,
+		Priority:  1,
+		IssueType: types.TypeGate,
+		Ephemeral: true,
+		AwaitType: "timer",
+		AwaitID:   "5s",
+		Timeout:   5 * time.Second,
+		Waiters:   []string{"system"},
+		CreatedAt: time.Now(),
+		UpdatedAt: time.Now(),
+	}
+	gate.ContentHash = gate.ComputeContentHash()
+
+	if err := store1.CreateIssue(ctx, gate, "daemon"); err != nil {
+		t.Fatalf("failed to create gate: %v", err)
+	}
+
+	// Verify gate was created with await fields
+	retrieved1, err := store1.GetIssue(ctx, gate.ID)
+	if err != nil || retrieved1 == nil {
+		t.Fatalf("failed to get gate from store1: %v", err)
+	}
+	if retrieved1.AwaitType != "timer" {
+		t.Errorf("store1: expected AwaitType=timer, got %q", retrieved1.AwaitType)
+	}
+	if retrieved1.AwaitID != "5s" {
+		t.Errorf("store1: expected AwaitID=5s, got %q", retrieved1.AwaitID)
+	}
+
+	// Close the first store (simulating daemon connection)
+	if err := store1.Close(); err != nil {
+		t.Fatalf("failed to close store1: %v", err)
+	}
+
+	// Step 2: Open a NEW connection to the same database
+	// (simulating `bd show --no-daemon` opening a new connection)
+	store2, err := New(ctx, dbPath)
+	if err != nil {
+		t.Fatalf("failed to create second store: %v", err)
+	}
+	defer store2.Close()
+
+	// Step 3: Read the gate from the new connection
+	// This should NOT clear the await fields
+	retrieved2, err := store2.GetIssue(ctx, gate.ID)
+	if err != nil || retrieved2 == nil {
+		t.Fatalf("failed to get gate from store2: %v", err)
+	}
+
+	// Verify await fields are PRESERVED
+	if retrieved2.AwaitType != "timer" {
+		t.Errorf("AwaitType was cleared! expected 'timer', got %q", retrieved2.AwaitType)
+	}
+	if retrieved2.AwaitID != "5s" {
+		t.Errorf("AwaitID was cleared! expected '5s', got %q", retrieved2.AwaitID)
+	}
+	if retrieved2.Timeout != 5*time.Second {
+		t.Errorf("Timeout was cleared! expected %v, got %v", 5*time.Second, retrieved2.Timeout)
+	}
+	if len(retrieved2.Waiters) != 1 || retrieved2.Waiters[0] != "system" {
+		t.Errorf("Waiters was cleared! expected [system], got %v", retrieved2.Waiters)
+	}
+}