fix: daemon delete creates tombstones, export includes tombstones (bd-rp4o)

Three changes to fix deleted issues resurrecting during bd sync:

1. daemon handleDelete now uses CreateTombstone instead of DeleteIssue
   - internal/rpc/server_issues_epics.go

2. sync.go exportToJSONL now includes IncludeTombstones:true
   - cmd/bd/sync.go

3. server_export_import_auto.go handleExport and auto-export now include
   tombstones in SearchIssues filter
   - internal/rpc/server_export_import_auto.go

Also adds README.md documentation for sync.branch mode (bd-dsdh):
- Explains "always dirty" working tree behavior
- Shell alias tip: gs='git status -- ":!.beads/"'
- When to use bd sync --merge

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

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

README.md

@@ -343,6 +343,48 @@ bd --no-auto-flush create "Issue"   # Skip auto-export
 bd --no-auto-import list            # Skip auto-import check
 ```
 
+### Sync Branch Mode (sync.branch)
+
+For protected branches or to reduce commit noise on main, configure a separate sync branch:
+
+```bash
+bd init --branch beads-sync    # During init
+# Or configure later:
+git config beads.sync.branch beads-sync
+```
+
+**How it works:**
+1. `bd sync` commits issue changes to the sync branch (e.g., `beads-sync`)
+2. Issue data is copied to your working tree so CLI commands work normally
+3. The sync branch accumulates commits; main stays clean
+4. Periodically merge with `bd sync --merge` (releases, milestones, etc.)
+
+**The "always dirty" working tree:**
+
+When sync.branch is configured, `.beads/issues.jsonl` in your working tree will **always appear modified**. This is by design:
+
+- bd copies the latest JSONL to your working tree so commands work
+- This copy is NOT committed to main (to reduce commit noise)
+- The file is "dirty" because it's newer than what's on main
+
+**Be Zen about it.** This is expected behavior, not a bug. Options:
+
+1. **Accept it** - Use a shell alias to hide beads from git status:
+   ```bash
+   alias gs='git status -- ":!.beads/"'
+   ```
+
+2. **Merge periodically** - Run `bd sync --merge` to snapshot issues to main:
+   ```bash
+   bd sync --merge              # Merge beads-sync → main
+   bd sync --merge --dry-run    # Preview what would be merged
+   ```
+
+3. **Disable sync.branch** - If clean working tree matters more:
+   ```bash
+   git config --unset beads.sync.branch
+   ```
+
 ## Hash-Based Issue IDs
 
 **Version 0.20.1 introduces collision-resistant hash-based IDs** to enable reliable multi-worker and multi-branch workflows.

cmd/bd/sync.go

@@ -1277,8 +1277,9 @@ func exportToJSONL(ctx context.Context, jsonlPath string) error {
 		return fmt.Errorf("failed to initialize store: %w", err)
 	}
 
-	// Get all issues
-	issues, err := store.SearchIssues(ctx, "", types.IssueFilter{})
+	// Get all issues including tombstones for sync propagation (bd-rp4o fix)
+	// Tombstones must be exported so they propagate to other clones and prevent resurrection
+	issues, err := store.SearchIssues(ctx, "", types.IssueFilter{IncludeTombstones: true})
 	if err != nil {
 		return fmt.Errorf("failed to get issues: %w", err)
 	}

internal/rpc/server_export_import_auto.go

@@ -49,8 +49,9 @@ func (s *Server) handleExport(req *Request) Response {
 		manifest = export.NewManifest(cfg.Policy)
 	}
 
-	// Get all issues (core operation, always fail-fast)
-	issues, err := store.SearchIssues(ctx, "", types.IssueFilter{})
+	// Get all issues including tombstones for sync propagation (bd-rp4o fix)
+	// Tombstones must be exported so they propagate to other clones and prevent resurrection
+	issues, err := store.SearchIssues(ctx, "", types.IssueFilter{IncludeTombstones: true})
 	if err != nil {
 		return Response{
 			Success: false,
@@ -464,8 +465,8 @@ func (s *Server) triggerExport(ctx context.Context, store storage.Storage, dbPat
 		}
 	}
 
-	// Export to JSONL (this will update the file with remapped IDs)
-	allIssues, err := sqliteStore.SearchIssues(ctx, "", types.IssueFilter{})
+	// Export to JSONL including tombstones for sync propagation (bd-rp4o fix)
+	allIssues, err := sqliteStore.SearchIssues(ctx, "", types.IssueFilter{IncludeTombstones: true})
 	if err != nil {
 		return fmt.Errorf("failed to fetch issues for export: %w", err)
 	}

internal/rpc/server_issues_epics.go

@@ -1,6 +1,7 @@
 package rpc
 
 import (
+	"context"
 	"encoding/json"
 	"fmt"
 	"os"
@@ -481,11 +482,27 @@ func (s *Server) handleDelete(req *Request) Response {
 			continue
 		}
 
-		// Delete the issue
+		// Create tombstone instead of hard delete (bd-rp4o fix)
+		// This preserves deletion history and prevents resurrection during sync
+		type tombstoner interface {
+			CreateTombstone(ctx context.Context, id string, actor string, reason string) error
+		}
+		if t, ok := store.(tombstoner); ok {
+			reason := deleteArgs.Reason
+			if reason == "" {
+				reason = "deleted via daemon"
+			}
+			if err := t.CreateTombstone(ctx, issueID, "daemon", reason); err != nil {
+				errors = append(errors, fmt.Sprintf("%s: %v", issueID, err))
+				continue
+			}
+		} else {
+			// Fallback to hard delete if CreateTombstone not available
 			if err := store.DeleteIssue(ctx, issueID); err != nil {
 				errors = append(errors, fmt.Sprintf("%s: %v", issueID, err))
 				continue
 			}
+		}
 
 		// Emit mutation event for event-driven daemon
 		s.emitMutation(MutationDelete, issueID)