fix(doctor,sync): clean up deletions manifest and reduce sync noise

- bd-8v5o: When doctor --fix hydrates issues from git history, also
  remove them from the deletions manifest to prevent perpetual skip
  warnings during sync

- bd-wsqt: Remove verbose per-issue "Skipping bd-xxx" messages during
  sync. Caller already shows summary of skipped issues.

Added RemoveDeletions() function to deletions package with tests.

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

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

cmd/bd/doctor/fix/migrate.go

@@ -36,6 +36,18 @@ func DatabaseVersion(path string) error {
 		if err := cmd.Run(); err != nil {
 			return fmt.Errorf("failed to initialize database: %w", err)
 		}
+
+		// bd-8v5o: Clean up deletions manifest for hydrated issues
+		// After init, remove any issues from deletions.jsonl that exist in JSONL
+		// This prevents perpetual "Skipping bd-xxx (in deletions manifest)" warnings
+		jsonlPath := findJSONLPath(beadsDir)
+		if jsonlPath != "" {
+			if err := cleanupDeletionsManifest(beadsDir, jsonlPath); err != nil {
+				// Non-fatal - just log warning
+				fmt.Printf("  Warning: failed to clean up deletions manifest: %v\n", err)
+			}
+		}
+
 		return nil
 	}
 
@@ -52,6 +64,22 @@ func DatabaseVersion(path string) error {
 	return nil
 }
 
+// findJSONLPath returns the path to the JSONL file in the beads directory.
+// Returns empty string if no JSONL file exists.
+func findJSONLPath(beadsDir string) string {
+	jsonlPath := filepath.Join(beadsDir, "issues.jsonl")
+	if _, err := os.Stat(jsonlPath); err == nil {
+		return jsonlPath
+	}
+
+	beadsJSONLPath := filepath.Join(beadsDir, "beads.jsonl")
+	if _, err := os.Stat(beadsJSONLPath); err == nil {
+		return beadsJSONLPath
+	}
+
+	return ""
+}
+
 // SchemaCompatibility fixes schema compatibility issues by running bd migrate
 func SchemaCompatibility(path string) error {
 	return DatabaseVersion(path)

cmd/bd/doctor/fix/sync.go

@@ -1,10 +1,14 @@
 package fix
 
 import (
+	"bufio"
+	"encoding/json"
 	"fmt"
 	"os"
 	"os/exec"
 	"path/filepath"
+
+	"github.com/steveyegge/beads/internal/deletions"
 )
 
 // DBJSONLSync fixes database-JSONL sync issues by running bd sync --import-only
@@ -27,10 +31,13 @@ func DBJSONLSync(path string) error {
 	}
 
 	hasJSONL := false
+	actualJSONLPath := ""
 	if _, err := os.Stat(jsonlPath); err == nil {
 		hasJSONL = true
+		actualJSONLPath = jsonlPath
 	} else if _, err := os.Stat(beadsJSONLPath); err == nil {
 		hasJSONL = true
+		actualJSONLPath = beadsJSONLPath
 	}
 
 	if !hasDB || !hasJSONL {
@@ -54,5 +61,107 @@ func DBJSONLSync(path string) error {
 		return fmt.Errorf("failed to sync database with JSONL: %w", err)
 	}
 
+	// bd-8v5o: Clean up deletions manifest for hydrated issues
+	// After sync, remove any issues from deletions.jsonl that exist in JSONL
+	// This prevents perpetual "Skipping bd-xxx (in deletions manifest)" warnings
+	if err := cleanupDeletionsManifest(beadsDir, actualJSONLPath); err != nil {
+		// Non-fatal - just log warning
+		fmt.Printf("  Warning: failed to clean up deletions manifest: %v\n", err)
+	}
+
 	return nil
 }
+
+// cleanupDeletionsManifest removes issues from deletions.jsonl that exist in JSONL.
+// This is needed because when issues are hydrated from git history (e.g., via bd init
+// or bd sync --import-only), they may still be in the deletions manifest from a
+// previous deletion. This causes perpetual skip warnings during sync.
+func cleanupDeletionsManifest(beadsDir, jsonlPath string) error {
+	deletionsPath := deletions.DefaultPath(beadsDir)
+
+	// Check if deletions manifest exists
+	if _, err := os.Stat(deletionsPath); os.IsNotExist(err) {
+		return nil // No deletions manifest, nothing to clean up
+	}
+
+	// Load deletions manifest
+	loadResult, err := deletions.LoadDeletions(deletionsPath)
+	if err != nil {
+		return fmt.Errorf("failed to load deletions manifest: %w", err)
+	}
+
+	if len(loadResult.Records) == 0 {
+		return nil // No deletions, nothing to clean up
+	}
+
+	// Get IDs from JSONL (excluding tombstones)
+	jsonlIDs, err := getNonTombstoneJSONLIDs(jsonlPath)
+	if err != nil {
+		return fmt.Errorf("failed to read JSONL: %w", err)
+	}
+
+	// Find IDs that are in both deletions manifest and JSONL
+	var idsToRemove []string
+	for id := range loadResult.Records {
+		if jsonlIDs[id] {
+			idsToRemove = append(idsToRemove, id)
+		}
+	}
+
+	if len(idsToRemove) == 0 {
+		return nil // No conflicting entries
+	}
+
+	// Remove conflicting entries from deletions manifest
+	result, err := deletions.RemoveDeletions(deletionsPath, idsToRemove)
+	if err != nil {
+		return fmt.Errorf("failed to remove deletions: %w", err)
+	}
+
+	if result.RemovedCount > 0 {
+		fmt.Printf("  Removed %d issue(s) from deletions manifest (now hydrated in JSONL)\n", result.RemovedCount)
+	}
+
+	return nil
+}
+
+// getNonTombstoneJSONLIDs reads the JSONL file and returns a set of IDs
+// that are not tombstones (status != "tombstone").
+func getNonTombstoneJSONLIDs(jsonlPath string) (map[string]bool, error) {
+	ids := make(map[string]bool)
+
+	file, err := os.Open(jsonlPath) // #nosec G304 - path validated by caller
+	if err != nil {
+		if os.IsNotExist(err) {
+			return ids, nil
+		}
+		return nil, err
+	}
+	defer func() {
+		_ = file.Close()
+	}()
+
+	scanner := bufio.NewScanner(file)
+	scanner.Buffer(make([]byte, 0, 64*1024), 10*1024*1024)
+
+	for scanner.Scan() {
+		line := scanner.Bytes()
+		if len(line) == 0 {
+			continue
+		}
+
+		var issue struct {
+			ID     string `json:"id"`
+			Status string `json:"status"`
+		}
+		if err := json.Unmarshal(line, &issue); err != nil {
+			continue
+		}
+		// Only include non-tombstone issues
+		if issue.ID != "" && issue.Status != "tombstone" {
+			ids[issue.ID] = true
+		}
+	}
+
+	return ids, scanner.Err()
+}