refactor: remove legacy autoflush code paths (bd-xsl9)

Remove dual code paths in the autoflush system. FlushManager is now the
only code path for auto-flush operations.

Changes:
- Remove legacy globals: isDirty, needsFullExport, flushTimer
- Remove flushToJSONL() wrapper function (was backward-compat shim)
- Simplify markDirtyAndScheduleFlush/FullExport to just call FlushManager
- Update tests to use FlushManager or flushToJSONLWithState directly

FlushManager handles all flush state internally in its run() goroutine,
eliminating the need for global state. Sandbox mode and tests that do
not need flushing get a no-op when FlushManager is nil.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

cmd/bd/main_test.go

@@ -16,9 +16,9 @@ import (
 	"github.com/steveyegge/beads/internal/types"
 )
 
-// TestAutoFlushOnExit tests that PersistentPostRun performs final flush before exit
+// TestAutoFlushOnExit tests that FlushManager.Shutdown() performs final flush before exit
 func TestAutoFlushOnExit(t *testing.T) {
-	// FIX: Initialize rootCtx for flush operations
+	// Initialize rootCtx for flush operations
 	ctx, cancel := context.WithTimeout(context.Background(), 30*time.Second)
 	defer cancel()
 
@@ -48,15 +48,16 @@ func TestAutoFlushOnExit(t *testing.T) {
 	storeActive = true
 	storeMutex.Unlock()
 
-	// Reset auto-flush state
+	// Initialize FlushManager for this test (short debounce for testing)
 	autoFlushEnabled = true
-	isDirty = false
-	if flushTimer != nil {
-		flushTimer.Stop()
-		flushTimer = nil
-	}
-
-	// ctx already declared above for rootCtx initialization
+	oldFlushManager := flushManager
+	flushManager = NewFlushManager(true, 50*time.Millisecond)
+	defer func() {
+		if flushManager != nil {
+			_ = flushManager.Shutdown()
+		}
+		flushManager = oldFlushManager
+	}()
 
 	// Create test issue
 	issue := &types.Issue{
@@ -75,50 +76,12 @@ func TestAutoFlushOnExit(t *testing.T) {
 	// Mark dirty (simulating CRUD operation)
 	markDirtyAndScheduleFlush()
 
-	// Simulate PersistentPostRun (exit behavior)
-	storeMutex.Lock()
-	storeActive = false
-	storeMutex.Unlock()
-
-	flushMutex.Lock()
-	needsFlush := isDirty && autoFlushEnabled
-	if needsFlush {
-		if flushTimer != nil {
-			flushTimer.Stop()
-			flushTimer = nil
-		}
-		isDirty = false
-	}
-	flushMutex.Unlock()
-
-	if needsFlush {
-		// Manually perform flush logic (simulating PersistentPostRun)
-		storeMutex.Lock()
-		storeActive = true // Temporarily re-enable for this test
-		storeMutex.Unlock()
-
-		issues, err := testStore.SearchIssues(ctx, "", types.IssueFilter{})
-		if err == nil {
-			allDeps, _ := testStore.GetAllDependencyRecords(ctx)
-			for _, iss := range issues {
-				iss.Dependencies = allDeps[iss.ID]
-			}
-			tempPath := jsonlPath + ".tmp"
-			f, err := os.Create(tempPath)
-			if err == nil {
-				encoder := json.NewEncoder(f)
-				for _, iss := range issues {
-					encoder.Encode(iss)
-				}
-				f.Close()
-				os.Rename(tempPath, jsonlPath)
-			}
-		}
-
-		storeMutex.Lock()
-		storeActive = false
-		storeMutex.Unlock()
+	// Simulate PersistentPostRun exit behavior - shutdown FlushManager
+	// This performs the final flush before exit
+	if err := flushManager.Shutdown(); err != nil {
+		t.Fatalf("FlushManager shutdown failed: %v", err)
 	}
+	flushManager = nil // Prevent double shutdown in defer
 
 	testStore.Close()
 
@@ -223,12 +186,8 @@ func TestAutoFlushJSONLContent(t *testing.T) {
 		}
 	}
 
-	// Mark dirty and flush immediately
-	flushMutex.Lock()
-	isDirty = true
-	flushMutex.Unlock()
-
-	flushToJSONL()
+	// Flush immediately (forces export)
+	flushToJSONLWithState(flushState{forceDirty: true})
 
 	// Verify JSONL file exists
 	if _, err := os.Stat(expectedJSONLPath); os.IsNotExist(err) {