refactor: remove all deletions.jsonl code (bd-fom)

Complete removal of the legacy deletions.jsonl manifest system.
Tombstones are now the sole deletion mechanism.

Removed:
- internal/deletions/ - entire package
- cmd/bd/deleted.go - deleted command
- cmd/bd/doctor/fix/deletions.go - HydrateDeletionsManifest
- Tests for all removed functionality

Cleaned:
- cmd/bd/sync.go - removed sanitize, auto-compact
- cmd/bd/delete.go - removed dual-writes
- cmd/bd/doctor.go - removed checkDeletionsManifest
- internal/importer/importer.go - removed deletions checks
- internal/syncbranch/worktree.go - removed deletions merge
- cmd/bd/integrity.go - updated validation (warn-only on decrease)

Files removed: 12
Lines removed: ~7500

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

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

cmd/bd/doctor/fix/sync.go

@@ -1,14 +1,10 @@
 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
@@ -31,13 +27,10 @@ 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 {
@@ -61,107 +54,5 @@ 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()
-}