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.

cmd/bd/test_repo_beads_guard_test.go

@@ -3,6 +3,7 @@ package main
 import (
 	"fmt"
 	"os"
+	"os/exec"
 	"path/filepath"
 	"testing"
 	"time"
@@ -15,12 +16,30 @@ func TestMain(m *testing.M) {
 	// This ensures backward compatibility with tests that manipulate globals directly.
 	enableTestModeGlobals()
 
+	// Prevent daemon auto-start and ensure tests don't interact with any running daemon.
+	// This prevents false positives in the test guard when a background daemon touches
+	// .beads files (like issues.jsonl via auto-sync) during test execution.
+	origNoDaemon := os.Getenv("BEADS_NO_DAEMON")
+	os.Setenv("BEADS_NO_DAEMON", "1")
+	defer func() {
+		if origNoDaemon != "" {
+			os.Setenv("BEADS_NO_DAEMON", origNoDaemon)
+		} else {
+			os.Unsetenv("BEADS_NO_DAEMON")
+		}
+	}()
+
 	if os.Getenv("BEADS_TEST_GUARD_DISABLE") != "" {
 		os.Exit(m.Run())
 	}
 
+	// Stop any running daemon for this repo to prevent false positives in the guard.
+	// The daemon auto-syncs and touches files like issues.jsonl, which would trigger
+	// the guard even though tests didn't cause the change.
 	repoRoot := findRepoRoot()
-	if repoRoot == "" {
+	if repoRoot != "" {
+		stopRepoDaemon(repoRoot)
+	} else {
 		os.Exit(m.Run())
 	}
 
@@ -120,3 +139,28 @@ func findRepoRoot() string {
 	}
 	return ""
 }
+
+// stopRepoDaemon stops any running daemon for the given repository.
+// This prevents false positives in the test guard when a background daemon
+// touches .beads files during test execution. Uses exec to avoid import cycles.
+func stopRepoDaemon(repoRoot string) {
+	beadsDir := filepath.Join(repoRoot, ".beads")
+	socketPath := filepath.Join(beadsDir, "bd.sock")
+
+	// Check if socket exists (quick check before shelling out)
+	if _, err := os.Stat(socketPath); err != nil {
+		return // no daemon running
+	}
+
+	// Shell out to bd daemon --stop. We can't call the daemon functions directly
+	// from TestMain because they have complex dependencies. Using exec is cleaner.
+	cmd := exec.Command("bd", "daemon", "--stop")
+	cmd.Dir = repoRoot
+	cmd.Env = append(os.Environ(), "BEADS_DIR="+beadsDir)
+
+	// Best-effort stop - ignore errors (daemon may not be running)
+	_ = cmd.Run()
+
+	// Give daemon time to shutdown gracefully
+	time.Sleep(500 * time.Millisecond)
+}