diff --git a/cmd/bd/sync.go b/cmd/bd/sync.go
index 989504b1..e95cd042 100644
--- a/cmd/bd/sync.go
+++ b/cmd/bd/sync.go
@@ -8,10 +8,12 @@ import (
 	"os/exec"
 	"path/filepath"
 	"sort"
+	"strconv"
 	"strings"
 	"time"
 
 	"github.com/spf13/cobra"
+	"github.com/steveyegge/beads/internal/deletions"
 	"github.com/steveyegge/beads/internal/rpc"
 	"github.com/steveyegge/beads/internal/syncbranch"
 	"github.com/steveyegge/beads/internal/types"
@@ -409,6 +411,12 @@ Use --merge to merge the sync branch back to main branch.`,
 		if dryRun {
 			fmt.Println("\n✓ Dry run complete (no changes made)")
 		} else {
+			// Auto-compact deletions manifest if enabled and threshold exceeded
+			if err := maybeAutoCompactDeletions(ctx, jsonlPath); err != nil {
+				// Non-fatal - just log warning
+				fmt.Fprintf(os.Stderr, "Warning: auto-compact deletions failed: %v\n", err)
+			}
+
 			fmt.Println("\n✓ Sync complete")
 		}
 	},
@@ -1105,11 +1113,84 @@ func importFromJSONL(ctx context.Context, jsonlPath string, renameOnImport bool)
 	if err != nil {
 		return fmt.Errorf("import failed: %w\n%s", err, output)
 	}
-	
+
 	// Show output (import command provides the summary)
 	if len(output) > 0 {
 		fmt.Print(string(output))
 	}
-	
+
+	return nil
+}
+
+// Default configuration values for auto-compact
+const (
+	defaultAutoCompact          = false
+	defaultAutoCompactThreshold = 1000
+)
+
+// maybeAutoCompactDeletions checks if auto-compact is enabled and threshold exceeded,
+// and if so, prunes the deletions manifest.
+func maybeAutoCompactDeletions(ctx context.Context, jsonlPath string) error {
+	// Ensure store is initialized for config access
+	if err := ensureStoreActive(); err != nil {
+		return nil // Can't access config, skip silently
+	}
+
+	// Check if auto-compact is enabled (disabled by default)
+	autoCompactStr, err := store.GetConfig(ctx, "deletions.auto_compact")
+	if err != nil || autoCompactStr == "" {
+		return nil // Not configured, skip
+	}
+
+	autoCompact := autoCompactStr == "true" || autoCompactStr == "1" || autoCompactStr == "yes"
+	if !autoCompact {
+		return nil // Disabled, skip
+	}
+
+	// Get threshold (default 1000)
+	threshold := defaultAutoCompactThreshold
+	if thresholdStr, err := store.GetConfig(ctx, "deletions.auto_compact_threshold"); err == nil && thresholdStr != "" {
+		if parsed, err := strconv.Atoi(thresholdStr); err == nil && parsed > 0 {
+			threshold = parsed
+		}
+	}
+
+	// Get deletions path
+	beadsDir := filepath.Dir(jsonlPath)
+	deletionsPath := deletions.DefaultPath(beadsDir)
+
+	// Count current deletions
+	count, err := deletions.Count(deletionsPath)
+	if err != nil {
+		return fmt.Errorf("failed to count deletions: %w", err)
+	}
+
+	// Check if threshold exceeded
+	if count <= threshold {
+		return nil // Below threshold, skip
+	}
+
+	// Get retention days (default 7)
+	retentionDays := deletions.DefaultRetentionDays
+	if retentionStr, err := store.GetConfig(ctx, "deletions.retention_days"); err == nil && retentionStr != "" {
+		if parsed, err := strconv.Atoi(retentionStr); err == nil && parsed > 0 {
+			retentionDays = parsed
+		}
+	}
+
+	// Prune deletions
+	fmt.Printf("→ Auto-compacting deletions manifest (%d entries > %d threshold)...\n", count, threshold)
+	result, err := deletions.PruneDeletions(deletionsPath, retentionDays)
+	if err != nil {
+		return fmt.Errorf("failed to prune deletions: %w", err)
+	}
+
+	if result.PrunedCount > 0 {
+		fmt.Printf("  Pruned %d entries older than %d days, kept %d entries\n",
+			result.PrunedCount, retentionDays, result.KeptCount)
+	} else {
+		fmt.Printf("  No entries older than %d days to prune\n", retentionDays)
+	}
+
 	return nil
 }
diff --git a/cmd/bd/sync_test.go b/cmd/bd/sync_test.go
index df5139c2..0bffbd5b 100644
--- a/cmd/bd/sync_test.go
+++ b/cmd/bd/sync_test.go
@@ -570,3 +570,221 @@ func TestZFCSkipsExportAfterImport(t *testing.T) {
 
 	t.Logf("✓ ZFC fix verified: DB synced from 100 to 10 issues, JSONL unchanged")
 }
+
+func TestMaybeAutoCompactDeletions_Disabled(t *testing.T) {
+	ctx := context.Background()
+	tmpDir := t.TempDir()
+
+	// Create test database
+	beadsDir := filepath.Join(tmpDir, ".beads")
+	if err := os.MkdirAll(beadsDir, 0755); err != nil {
+		t.Fatalf("failed to create beads dir: %v", err)
+	}
+
+	testDBPath := filepath.Join(beadsDir, "beads.db")
+	jsonlPath := filepath.Join(beadsDir, "beads.jsonl")
+
+	// Create store
+	testStore, err := sqlite.New(ctx, testDBPath)
+	if err != nil {
+		t.Fatalf("failed to create store: %v", err)
+	}
+	defer testStore.Close()
+
+	// Set global store for maybeAutoCompactDeletions
+	// Save and restore original values
+	originalStore := store
+	originalStoreActive := storeActive
+	defer func() {
+		store = originalStore
+		storeActive = originalStoreActive
+	}()
+
+	store = testStore
+	storeActive = true
+
+	// Create empty JSONL file
+	if err := os.WriteFile(jsonlPath, []byte{}, 0644); err != nil {
+		t.Fatalf("failed to create JSONL: %v", err)
+	}
+
+	// Auto-compact is disabled by default, so should return nil
+	err = maybeAutoCompactDeletions(ctx, jsonlPath)
+	if err != nil {
+		t.Errorf("expected no error when auto-compact disabled, got: %v", err)
+	}
+}
+
+func TestMaybeAutoCompactDeletions_Enabled(t *testing.T) {
+	ctx := context.Background()
+	tmpDir := t.TempDir()
+
+	// Create test database
+	beadsDir := filepath.Join(tmpDir, ".beads")
+	if err := os.MkdirAll(beadsDir, 0755); err != nil {
+		t.Fatalf("failed to create beads dir: %v", err)
+	}
+
+	testDBPath := filepath.Join(beadsDir, "beads.db")
+	jsonlPath := filepath.Join(beadsDir, "beads.jsonl")
+	deletionsPath := filepath.Join(beadsDir, "deletions.jsonl")
+
+	// Create store
+	testStore, err := sqlite.New(ctx, testDBPath)
+	if err != nil {
+		t.Fatalf("failed to create store: %v", err)
+	}
+	defer testStore.Close()
+
+	// Enable auto-compact with low threshold
+	if err := testStore.SetConfig(ctx, "deletions.auto_compact", "true"); err != nil {
+		t.Fatalf("failed to set auto_compact config: %v", err)
+	}
+	if err := testStore.SetConfig(ctx, "deletions.auto_compact_threshold", "5"); err != nil {
+		t.Fatalf("failed to set threshold config: %v", err)
+	}
+	if err := testStore.SetConfig(ctx, "deletions.retention_days", "1"); err != nil {
+		t.Fatalf("failed to set retention config: %v", err)
+	}
+
+	// Set global store for maybeAutoCompactDeletions
+	// Save and restore original values
+	originalStore := store
+	originalStoreActive := storeActive
+	defer func() {
+		store = originalStore
+		storeActive = originalStoreActive
+	}()
+
+	store = testStore
+	storeActive = true
+
+	// Create empty JSONL file
+	if err := os.WriteFile(jsonlPath, []byte{}, 0644); err != nil {
+		t.Fatalf("failed to create JSONL: %v", err)
+	}
+
+	// Create deletions file with entries (some old, some recent)
+	now := time.Now()
+	deletionsContent := ""
+	// Add 10 old entries (will be pruned)
+	for i := 0; i < 10; i++ {
+		oldTime := now.AddDate(0, 0, -10).Format(time.RFC3339)
+		deletionsContent += fmt.Sprintf(`{"id":"bd-old-%d","ts":"%s","by":"user"}`, i, oldTime) + "\n"
+	}
+	// Add 3 recent entries (will be kept)
+	for i := 0; i < 3; i++ {
+		recentTime := now.Add(-1 * time.Hour).Format(time.RFC3339)
+		deletionsContent += fmt.Sprintf(`{"id":"bd-recent-%d","ts":"%s","by":"user"}`, i, recentTime) + "\n"
+	}
+
+	if err := os.WriteFile(deletionsPath, []byte(deletionsContent), 0644); err != nil {
+		t.Fatalf("failed to create deletions file: %v", err)
+	}
+
+	// Verify initial count
+	initialCount := strings.Count(deletionsContent, "\n")
+	if initialCount != 13 {
+		t.Fatalf("expected 13 initial entries, got %d", initialCount)
+	}
+
+	// Run auto-compact
+	err = maybeAutoCompactDeletions(ctx, jsonlPath)
+	if err != nil {
+		t.Errorf("auto-compact failed: %v", err)
+	}
+
+	// Read deletions file and count remaining entries
+	afterContent, err := os.ReadFile(deletionsPath)
+	if err != nil {
+		t.Fatalf("failed to read deletions file: %v", err)
+	}
+
+	afterLines := strings.Split(strings.TrimSpace(string(afterContent)), "\n")
+	afterCount := 0
+	for _, line := range afterLines {
+		if line != "" {
+			afterCount++
+		}
+	}
+
+	// Should have pruned old entries, kept recent ones
+	if afterCount != 3 {
+		t.Errorf("expected 3 entries after prune (recent ones), got %d", afterCount)
+	}
+}
+
+func TestMaybeAutoCompactDeletions_BelowThreshold(t *testing.T) {
+	ctx := context.Background()
+	tmpDir := t.TempDir()
+
+	// Create test database
+	beadsDir := filepath.Join(tmpDir, ".beads")
+	if err := os.MkdirAll(beadsDir, 0755); err != nil {
+		t.Fatalf("failed to create beads dir: %v", err)
+	}
+
+	testDBPath := filepath.Join(beadsDir, "beads.db")
+	jsonlPath := filepath.Join(beadsDir, "beads.jsonl")
+	deletionsPath := filepath.Join(beadsDir, "deletions.jsonl")
+
+	// Create store
+	testStore, err := sqlite.New(ctx, testDBPath)
+	if err != nil {
+		t.Fatalf("failed to create store: %v", err)
+	}
+	defer testStore.Close()
+
+	// Enable auto-compact with high threshold
+	if err := testStore.SetConfig(ctx, "deletions.auto_compact", "true"); err != nil {
+		t.Fatalf("failed to set auto_compact config: %v", err)
+	}
+	if err := testStore.SetConfig(ctx, "deletions.auto_compact_threshold", "100"); err != nil {
+		t.Fatalf("failed to set threshold config: %v", err)
+	}
+
+	// Set global store for maybeAutoCompactDeletions
+	// Save and restore original values
+	originalStore := store
+	originalStoreActive := storeActive
+	defer func() {
+		store = originalStore
+		storeActive = originalStoreActive
+	}()
+
+	store = testStore
+	storeActive = true
+
+	// Create empty JSONL file
+	if err := os.WriteFile(jsonlPath, []byte{}, 0644); err != nil {
+		t.Fatalf("failed to create JSONL: %v", err)
+	}
+
+	// Create deletions file with only 5 entries (below threshold of 100)
+	now := time.Now()
+	deletionsContent := ""
+	for i := 0; i < 5; i++ {
+		ts := now.Add(-1 * time.Hour).Format(time.RFC3339)
+		deletionsContent += fmt.Sprintf(`{"id":"bd-%d","ts":"%s","by":"user"}`, i, ts) + "\n"
+	}
+
+	if err := os.WriteFile(deletionsPath, []byte(deletionsContent), 0644); err != nil {
+		t.Fatalf("failed to create deletions file: %v", err)
+	}
+
+	// Run auto-compact - should skip because below threshold
+	err = maybeAutoCompactDeletions(ctx, jsonlPath)
+	if err != nil {
+		t.Errorf("auto-compact failed: %v", err)
+	}
+
+	// Read deletions file - should be unchanged
+	afterContent, err := os.ReadFile(deletionsPath)
+	if err != nil {
+		t.Fatalf("failed to read deletions file: %v", err)
+	}
+
+	if string(afterContent) != deletionsContent {
+		t.Error("deletions file should not be modified when below threshold")
+	}
+}
diff --git a/internal/deletions/deletions.go b/internal/deletions/deletions.go
index a25875ec..af1c1699 100644
--- a/internal/deletions/deletions.go
+++ b/internal/deletions/deletions.go
@@ -180,6 +180,35 @@ func DefaultPath(beadsDir string) string {
 	return filepath.Join(beadsDir, "deletions.jsonl")
 }
 
+// Count returns the number of lines in the deletions manifest.
+// This is a fast operation that doesn't parse JSON, just counts lines.
+// Returns 0 if the file doesn't exist or is empty.
+func Count(path string) (int, error) {
+	f, err := os.Open(path) // #nosec G304 - controlled path from caller
+	if err != nil {
+		if os.IsNotExist(err) {
+			return 0, nil
+		}
+		return 0, fmt.Errorf("failed to open deletions file: %w", err)
+	}
+	defer f.Close()
+
+	count := 0
+	scanner := bufio.NewScanner(f)
+	for scanner.Scan() {
+		line := scanner.Text()
+		if line != "" {
+			count++
+		}
+	}
+
+	if err := scanner.Err(); err != nil {
+		return 0, fmt.Errorf("error reading deletions file: %w", err)
+	}
+
+	return count, nil
+}
+
 // DefaultRetentionDays is the default number of days to retain deletion records.
 const DefaultRetentionDays = 7
 
diff --git a/internal/deletions/deletions_test.go b/internal/deletions/deletions_test.go
index ecb588a3..bfeb6f23 100644
--- a/internal/deletions/deletions_test.go
+++ b/internal/deletions/deletions_test.go
@@ -546,3 +546,64 @@ func TestPruneDeletions_ZeroRetention(t *testing.T) {
 		t.Errorf("expected 1 pruned with 0 retention, got %d", result.PrunedCount)
 	}
 }
+
+func TestCount_Empty(t *testing.T) {
+	// Non-existent file should return 0
+	count, err := Count("/nonexistent/path/deletions.jsonl")
+	if err != nil {
+		t.Fatalf("expected no error for non-existent file, got: %v", err)
+	}
+	if count != 0 {
+		t.Errorf("expected 0 count for non-existent file, got %d", count)
+	}
+}
+
+func TestCount_WithRecords(t *testing.T) {
+	tmpDir := t.TempDir()
+	path := filepath.Join(tmpDir, "deletions.jsonl")
+
+	now := time.Now()
+	records := []DeletionRecord{
+		{ID: "bd-001", Timestamp: now, Actor: "user1"},
+		{ID: "bd-002", Timestamp: now, Actor: "user2"},
+		{ID: "bd-003", Timestamp: now, Actor: "user3"},
+	}
+
+	for _, r := range records {
+		if err := AppendDeletion(path, r); err != nil {
+			t.Fatalf("AppendDeletion failed: %v", err)
+		}
+	}
+
+	count, err := Count(path)
+	if err != nil {
+		t.Fatalf("Count failed: %v", err)
+	}
+	if count != 3 {
+		t.Errorf("expected 3, got %d", count)
+	}
+}
+
+func TestCount_WithEmptyLines(t *testing.T) {
+	tmpDir := t.TempDir()
+	path := filepath.Join(tmpDir, "deletions.jsonl")
+
+	// Write content with empty lines
+	content := `{"id":"bd-001","ts":"2024-01-01T00:00:00Z","by":"user1"}
+
+{"id":"bd-002","ts":"2024-01-02T00:00:00Z","by":"user2"}
+
+`
+	if err := os.WriteFile(path, []byte(content), 0644); err != nil {
+		t.Fatalf("failed to write test file: %v", err)
+	}
+
+	count, err := Count(path)
+	if err != nil {
+		t.Fatalf("Count failed: %v", err)
+	}
+	// Should count only non-empty lines
+	if count != 2 {
+		t.Errorf("expected 2 (excluding empty lines), got %d", count)
+	}
+}
diff --git a/internal/importer/importer.go b/internal/importer/importer.go
index cd8a7487..d54dad35 100644
--- a/internal/importer/importer.go
+++ b/internal/importer/importer.go
@@ -7,6 +7,7 @@ import (
 	"os"
 	"os/exec"
 	"path/filepath"
+	"regexp"
 	"sort"
 	"strings"
 	"time"
@@ -862,11 +863,34 @@ func checkGitHistoryForDeletions(beadsDir string, ids []string) []string {
 		return nil
 	}
 
-	// Get the repo root directory (parent of .beads)
-	repoRoot := filepath.Dir(beadsDir)
+	// Find the actual git repo root using git rev-parse (bd-bhd)
+	// This handles monorepos and nested projects where .beads isn't at repo root
+	ctx, cancel := context.WithTimeout(context.Background(), 5*time.Second)
+	defer cancel()
+
+	cmd := exec.CommandContext(ctx, "git", "rev-parse", "--show-toplevel")
+	cmd.Dir = beadsDir
+	output, err := cmd.Output()
+	if err != nil {
+		// Not in a git repo or git not available - can't do history check
+		return nil
+	}
+	repoRoot := strings.TrimSpace(string(output))
+
+	// Compute relative path from repo root to beads.jsonl
+	// beadsDir is absolute, compute its path relative to repoRoot
+	absBeadsDir, err := filepath.Abs(beadsDir)
+	if err != nil {
+		return nil
+	}
+
+	relBeadsDir, err := filepath.Rel(repoRoot, absBeadsDir)
+	if err != nil {
+		return nil
+	}
 
 	// Build JSONL path relative to repo root
-	jsonlPath := filepath.Join(".beads", "beads.jsonl")
+	jsonlPath := filepath.Join(relBeadsDir, "beads.jsonl")
 
 	var deleted []string
 
@@ -888,15 +912,24 @@ func checkGitHistoryForDeletions(beadsDir string, ids []string) []string {
 	return deleted
 }
 
+// gitHistoryTimeout is the maximum time to wait for git history searches.
+// Prevents hangs on large repositories (bd-f0n).
+const gitHistoryTimeout = 30 * time.Second
+
 // wasInGitHistory checks if a single ID was ever in the JSONL via git history.
 // Returns true if the ID was found in history (meaning it was deleted).
 func wasInGitHistory(repoRoot, jsonlPath, id string) bool {
 	// git log --all -S "\"id\":\"bd-xxx\"" --oneline -- .beads/beads.jsonl
 	// This searches for commits that added or removed the ID string
+	// Note: -S uses literal string matching, not regex, so no escaping needed
 	searchPattern := fmt.Sprintf(`"id":"%s"`, id)
 
+	// Use context with timeout to prevent hangs on large repos (bd-f0n)
+	ctx, cancel := context.WithTimeout(context.Background(), gitHistoryTimeout)
+	defer cancel()
+
 	// #nosec G204 - searchPattern is constructed from validated issue IDs
-	cmd := exec.Command("git", "log", "--all", "-S", searchPattern, "--oneline", "--", jsonlPath)
+	cmd := exec.CommandContext(ctx, "git", "log", "--all", "-S", searchPattern, "--oneline", "--", jsonlPath)
 	cmd.Dir = repoRoot
 
 	var stdout bytes.Buffer
@@ -904,7 +937,7 @@ func wasInGitHistory(repoRoot, jsonlPath, id string) bool {
 	cmd.Stderr = nil // Ignore stderr
 
 	if err := cmd.Run(); err != nil {
-		// Git command failed - could be shallow clone, not a git repo, etc.
+		// Git command failed - could be shallow clone, not a git repo, timeout, etc.
 		// Conservative: assume issue is local work, don't delete
 		return false
 	}
@@ -919,15 +952,21 @@ func wasInGitHistory(repoRoot, jsonlPath, id string) bool {
 func batchCheckGitHistory(repoRoot, jsonlPath string, ids []string) []string {
 	// Build a regex pattern to match any of the IDs
 	// Pattern: "id":"bd-xxx"|"id":"bd-yyy"|...
+	// Escape regex special characters in IDs to avoid malformed patterns (bd-bgs)
 	patterns := make([]string, 0, len(ids))
 	for _, id := range ids {
-		patterns = append(patterns, fmt.Sprintf(`"id":"%s"`, id))
+		escapedID := regexp.QuoteMeta(id)
+		patterns = append(patterns, fmt.Sprintf(`"id":"%s"`, escapedID))
 	}
 	searchPattern := strings.Join(patterns, "|")
 
+	// Use context with timeout to prevent hangs on large repos (bd-f0n)
+	ctx, cancel := context.WithTimeout(context.Background(), gitHistoryTimeout)
+	defer cancel()
+
 	// Use git log -G (regex) for batch search
 	// #nosec G204 - searchPattern is constructed from validated issue IDs
-	cmd := exec.Command("git", "log", "--all", "-G", searchPattern, "-p", "--", jsonlPath)
+	cmd := exec.CommandContext(ctx, "git", "log", "--all", "-G", searchPattern, "-p", "--", jsonlPath)
 	cmd.Dir = repoRoot
 
 	var stdout bytes.Buffer
@@ -935,7 +974,8 @@ func batchCheckGitHistory(repoRoot, jsonlPath string, ids []string) []string {
 	cmd.Stderr = nil // Ignore stderr
 
 	if err := cmd.Run(); err != nil {
-		// Git command failed - fall back to individual checks
+		// Git command failed (timeout, shallow clone, etc.) - fall back to individual checks
+		// Individual checks also have timeout protection
 		var deleted []string
 		for _, id := range ids {
 			if wasInGitHistory(repoRoot, jsonlPath, id) {