Fix P1 deletion tracking bugs (bd-rbxi)

- bd-nqes: Made snapshot capture mandatory with fail-fast
- bd-mn9p: Added semantic JSON comparison (jsonEquals)
- bd-2ifg: Collect deletion errors and fail operation
- bd-8ayj: Atomic file ops with PID-specific temp files
- bd-aewm: Added defer cleanup for .merged temp file

All tests pass.

Amp-Thread-ID: https://ampcode.com/threads/T-5e744954-8a08-4697-960e-5f2a88d50c54
Co-authored-by: Amp <amp@ampcode.com>

cmd/bd/daemon_sync.go

@@ -500,8 +500,10 @@ func createSyncFunc(ctx context.Context, store storage.Storage, autoCommit, auto
 		log.log("Exported to JSONL")
 
 		// Capture left snapshot (pre-pull state) for 3-way merge
+		// This is mandatory for deletion tracking integrity
 		if err := captureLeftSnapshot(jsonlPath); err != nil {
-			log.log("Warning: failed to capture snapshot for deletion tracking: %v", err)
+			log.log("Error: failed to capture snapshot (required for deletion tracking): %v", err)
+			return
 		}
 
 		if autoCommit {

cmd/bd/deletion_tracking.go

@@ -8,11 +8,24 @@ import (
 	"io"
 	"os"
 	"path/filepath"
+	"reflect"
 
 	"github.com/steveyegge/beads/internal/merge"
 	"github.com/steveyegge/beads/internal/storage"
 )
 
+// jsonEquals compares two JSON strings semantically, handling field reordering
+func jsonEquals(a, b string) bool {
+	var objA, objB map[string]interface{}
+	if err := json.Unmarshal([]byte(a), &objA); err != nil {
+		return false
+	}
+	if err := json.Unmarshal([]byte(b), &objB); err != nil {
+		return false
+	}
+	return reflect.DeepEqual(objA, objB)
+}
+
 // getSnapshotPaths returns paths for base and left snapshot files
 func getSnapshotPaths(jsonlPath string) (basePath, leftPath string) {
 	dir := filepath.Dir(jsonlPath)
@@ -23,16 +36,30 @@ func getSnapshotPaths(jsonlPath string) (basePath, leftPath string) {
 
 // captureLeftSnapshot copies the current JSONL to the left snapshot file
 // This should be called after export, before git pull
+// Uses atomic file operations to prevent race conditions
 func captureLeftSnapshot(jsonlPath string) error {
 	_, leftPath := getSnapshotPaths(jsonlPath)
-	return copyFileSnapshot(jsonlPath, leftPath)
+	// Use process-specific temp file to prevent concurrent write conflicts
+	tempPath := fmt.Sprintf("%s.%d.tmp", leftPath, os.Getpid())
+	if err := copyFileSnapshot(jsonlPath, tempPath); err != nil {
+		return err
+	}
+	// Atomic rename on POSIX systems
+	return os.Rename(tempPath, leftPath)
 }
 
 // updateBaseSnapshot copies the current JSONL to the base snapshot file
 // This should be called after successful import to track the new baseline
+// Uses atomic file operations to prevent race conditions
 func updateBaseSnapshot(jsonlPath string) error {
 	basePath, _ := getSnapshotPaths(jsonlPath)
-	return copyFileSnapshot(jsonlPath, basePath)
+	// Use process-specific temp file to prevent concurrent write conflicts
+	tempPath := fmt.Sprintf("%s.%d.tmp", basePath, os.Getpid())
+	if err := copyFileSnapshot(jsonlPath, tempPath); err != nil {
+		return err
+	}
+	// Atomic rename on POSIX systems
+	return os.Rename(tempPath, basePath)
 }
 
 // merge3WayAndPruneDeletions performs 3-way merge and prunes accepted deletions from DB
@@ -47,6 +74,13 @@ func merge3WayAndPruneDeletions(ctx context.Context, store storage.Storage, json
 
 	// Run 3-way merge: base (last import) vs left (pre-pull export) vs right (pulled JSONL)
 	tmpMerged := jsonlPath + ".merged"
+	// Ensure temp file cleanup on failure
+	defer func() {
+		if fileExists(tmpMerged) {
+			os.Remove(tmpMerged)
+		}
+	}()
+
 	err := merge.Merge3Way(tmpMerged, basePath, leftPath, jsonlPath, false)
 	if err != nil {
 		// Merge error (including conflicts) is returned as error
@@ -70,15 +104,21 @@ func merge3WayAndPruneDeletions(ctx context.Context, store storage.Storage, json
 		DeleteIssue(context.Context, string) error
 	}
 
-	for _, id := range acceptedDeletions {
-		if d, ok := store.(deleter); ok {
-			if err := d.DeleteIssue(ctx, id); err != nil {
-				// Log warning but continue - issue might already be deleted
-				fmt.Fprintf(os.Stderr, "Warning: failed to delete issue %s during merge: %v\n", id, err)
-			}
-		} else {
+	d, ok := store.(deleter)
+	if !ok {
 		return false, fmt.Errorf("storage backend does not support DeleteIssue")
 	}
+
+	// Collect all deletion errors - fail the operation if any delete fails
+	var deletionErrors []error
+	for _, id := range acceptedDeletions {
+		if err := d.DeleteIssue(ctx, id); err != nil {
+			deletionErrors = append(deletionErrors, fmt.Errorf("issue %s: %w", id, err))
+		}
+	}
+
+	if len(deletionErrors) > 0 {
+		return false, fmt.Errorf("deletion failures (DB may be inconsistent): %v", deletionErrors)
 	}
 
 	if len(acceptedDeletions) > 0 {
@@ -121,8 +161,8 @@ func computeAcceptedDeletions(basePath, leftPath, mergedPath string) ([]string,
 	for id, baseLine := range baseIndex {
 		// Issue in base but not in merged
 		if !mergedIDs[id] {
-			// Check if unchanged locally (leftLine == baseLine)
-			if leftLine, existsInLeft := leftIndex[id]; existsInLeft && leftLine == baseLine {
+			// Check if unchanged locally using semantic JSON comparison
+			if leftLine, existsInLeft := leftIndex[id]; existsInLeft && jsonEquals(leftLine, baseLine) {
 				deletions = append(deletions, id)
 			}
 		}

cmd/bd/sync.go

@@ -150,8 +150,10 @@ Use --merge to merge the sync branch back to main branch.`,
 			}
 
 			// Capture left snapshot (pre-pull state) for 3-way merge
+			// This is mandatory for deletion tracking integrity
 			if err := captureLeftSnapshot(jsonlPath); err != nil {
-				fmt.Fprintf(os.Stderr, "Warning: failed to capture snapshot for deletion tracking: %v\n", err)
+				fmt.Fprintf(os.Stderr, "Error: failed to capture snapshot (required for deletion tracking): %v\n", err)
+				os.Exit(1)
 			}
 		}