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)