feat(deletions): add pruning and git history fallback

Implements two P1 tasks for the deletions manifest epic:

bd-v2x: Add deletions pruning to bd compact
- PruneDeletions function removes records older than retention period
- Default retention: 7 days (configurable via metadata.json)
- CLI --retention flag for override
- Atomic file rewrite prevents corruption
- Called automatically during all compact operations

bd-pnm: Add git history fallback for pruned deletions
- Catches deletions where manifest entry was pruned
- Uses git log -S to search for ID in JSONL history
- Batches multiple IDs for efficiency (git -G regex)
- Self-healing: backfills manifest on hit
- Conservative: keeps issue if git check fails (shallow clone)

Tests added for both features with edge cases covered.

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

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

internal/configfile/configfile.go

@@ -13,6 +13,9 @@ type Config struct {
 	Database      string `json:"database"`
 	JSONLExport   string `json:"jsonl_export,omitempty"`
 	LastBdVersion string `json:"last_bd_version,omitempty"`
+
+	// Deletions configuration
+	DeletionsRetentionDays int `json:"deletions_retention_days,omitempty"` // 0 means use default (7 days)
 }
 
 func DefaultConfig() *Config {
@@ -94,3 +97,14 @@ func (c *Config) JSONLPath(beadsDir string) string {
 	}
 	return filepath.Join(beadsDir, c.JSONLExport)
 }
+
+// DefaultDeletionsRetentionDays is the default retention period for deletion records.
+const DefaultDeletionsRetentionDays = 7
+
+// GetDeletionsRetentionDays returns the configured retention days, or the default if not set.
+func (c *Config) GetDeletionsRetentionDays() int {
+	if c.DeletionsRetentionDays <= 0 {
+		return DefaultDeletionsRetentionDays
+	}
+	return c.DeletionsRetentionDays
+}

internal/configfile/configfile_test.go

@@ -114,8 +114,46 @@ func TestConfigPath(t *testing.T) {
 	beadsDir := "/home/user/project/.beads"
 	got := ConfigPath(beadsDir)
 	want := filepath.Join(beadsDir, "metadata.json")
-	
+
 	if got != want {
 		t.Errorf("ConfigPath() = %q, want %q", got, want)
 	}
 }
+
+func TestGetDeletionsRetentionDays(t *testing.T) {
+	tests := []struct {
+		name   string
+		cfg    *Config
+		want   int
+	}{
+		{
+			name: "zero uses default",
+			cfg:  &Config{DeletionsRetentionDays: 0},
+			want: DefaultDeletionsRetentionDays,
+		},
+		{
+			name: "negative uses default",
+			cfg:  &Config{DeletionsRetentionDays: -5},
+			want: DefaultDeletionsRetentionDays,
+		},
+		{
+			name: "custom value",
+			cfg:  &Config{DeletionsRetentionDays: 14},
+			want: 14,
+		},
+		{
+			name: "minimum value 1",
+			cfg:  &Config{DeletionsRetentionDays: 1},
+			want: 1,
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			got := tt.cfg.GetDeletionsRetentionDays()
+			if got != tt.want {
+				t.Errorf("GetDeletionsRetentionDays() = %d, want %d", got, tt.want)
+			}
+		})
+	}
+}