feat(storage): add Dolt backend for version-controlled issue storage

Implements a complete Dolt storage backend that mirrors the SQLite implementation
with MySQL-compatible syntax and adds version control capabilities.

Key features:
- Full Storage interface implementation (~50 methods)
- Version control operations: commit, push, pull, branch, merge, checkout
- History queries via AS OF and dolt_history_* tables
- Cell-level merge instead of line-level JSONL merge
- SQL injection protection with input validation

Bug fixes applied during implementation:
- Added missing quality_score, work_type, source_system to scanIssue
- Fixed Status() to properly parse boolean staged column
- Added validation to CreateIssues (was missing in batch create)
- Made RenameDependencyPrefix transactional
- Expanded GetIssueHistory to return more complete data

Test coverage: 17 tests covering CRUD, dependencies, labels, search,
comments, events, statistics, and SQL injection protection.

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

go.mod

@@ -27,12 +27,27 @@ require (
 )
 
 require (
+	cloud.google.com/go v0.115.0 // indirect
+	cloud.google.com/go/auth v0.7.2 // indirect
+	cloud.google.com/go/auth/oauth2adapt v0.2.3 // indirect
+	cloud.google.com/go/compute/metadata v0.5.0 // indirect
+	cloud.google.com/go/iam v1.1.10 // indirect
+	cloud.google.com/go/storage v1.41.0 // indirect
+	filippo.io/edwards25519 v1.1.0 // indirect
 	github.com/AlekSi/pointer v1.0.0 // indirect
+	github.com/HdrHistogram/hdrhistogram-go v1.1.2 // indirect
 	github.com/alecthomas/chroma/v2 v2.14.0 // indirect
+	github.com/aliyun/aliyun-oss-go-sdk v3.0.2+incompatible // indirect
+	github.com/apache/arrow/go/arrow v0.0.0-20211112161151-bc219186db40 // indirect
+	github.com/apache/thrift v0.19.0 // indirect
 	github.com/atotto/clipboard v0.1.4 // indirect
+	github.com/aws/aws-sdk-go v1.50.16 // indirect
 	github.com/aymanbagabas/go-osc52/v2 v2.0.1 // indirect
 	github.com/aymerick/douceur v0.2.0 // indirect
+	github.com/bcicen/jstream v1.0.1 // indirect
 	github.com/catppuccin/go v0.3.0 // indirect
+	github.com/cenkalti/backoff/v4 v4.2.1 // indirect
+	github.com/cespare/xxhash/v2 v2.2.0 // indirect
 	github.com/charmbracelet/bubbles v0.21.1-0.20250623103423-23b8fd6302d7 // indirect
 	github.com/charmbracelet/bubbletea v1.3.6 // indirect
 	github.com/charmbracelet/colorprofile v0.2.3-0.20250311203215-f60798e515dc // indirect
@@ -41,27 +56,75 @@ require (
 	github.com/charmbracelet/x/exp/slice v0.0.0-20250327172914-2fdc97757edf // indirect
 	github.com/charmbracelet/x/exp/strings v0.0.0-20240722160745-212f7b056ed0 // indirect
 	github.com/charmbracelet/x/term v0.2.1 // indirect
+	github.com/denisbrodbeck/machineid v1.0.1 // indirect
 	github.com/dlclark/regexp2 v1.11.0 // indirect
+	github.com/dolthub/dolt/go v0.40.5-0.20240702155756-bcf4dd5f5cc1 // indirect
+	github.com/dolthub/dolt/go/gen/proto/dolt/services/eventsapi v0.0.0-20240212175631-02e9f99a3a9b // indirect
+	github.com/dolthub/driver v0.2.0 // indirect
+	github.com/dolthub/flatbuffers/v23 v23.3.3-dh.2 // indirect
+	github.com/dolthub/fslock v0.0.3 // indirect
+	github.com/dolthub/go-icu-regex v0.0.0-20230524105445-af7e7991c97e // indirect
+	github.com/dolthub/go-mysql-server v0.18.2-0.20240702022058-d7eb602c04ee // indirect
+	github.com/dolthub/gozstd v0.0.0-20240423170813-23a2903bca63 // indirect
+	github.com/dolthub/jsonpath v0.0.2-0.20240227200619-19675ab05c71 // indirect
+	github.com/dolthub/maphash v0.1.0 // indirect
+	github.com/dolthub/swiss v0.2.1 // indirect
+	github.com/dolthub/vitess v0.0.0-20240709194214-7926ea9d425d // indirect
 	github.com/dustin/go-humanize v1.0.1 // indirect
 	github.com/erikgeiser/coninput v0.0.0-20211004153227-1c3628e74d0f // indirect
+	github.com/fatih/color v1.16.0 // indirect
+	github.com/felixge/httpsnoop v1.0.4 // indirect
+	github.com/go-kit/kit v0.13.0 // indirect
+	github.com/go-logr/logr v1.4.2 // indirect
+	github.com/go-logr/stdr v1.2.2 // indirect
+	github.com/go-sql-driver/mysql v1.7.2-0.20231213112541-0004702b931d // indirect
 	github.com/go-viper/mapstructure/v2 v2.4.0 // indirect
+	github.com/goccy/go-json v0.10.2 // indirect
+	github.com/golang/groupcache v0.0.0-20210331224755-41bb18bfe9da // indirect
+	github.com/golang/protobuf v1.5.4 // indirect
+	github.com/golang/snappy v0.0.4 // indirect
+	github.com/google/btree v1.1.2 // indirect
 	github.com/google/go-cmp v0.7.0 // indirect
+	github.com/google/s2a-go v0.1.7 // indirect
+	github.com/google/uuid v1.6.0 // indirect
+	github.com/googleapis/enterprise-certificate-proxy v0.3.2 // indirect
+	github.com/googleapis/gax-go/v2 v2.12.5 // indirect
 	github.com/gorilla/css v1.0.1 // indirect
+	github.com/hashicorp/golang-lru v1.0.2 // indirect
+	github.com/hashicorp/golang-lru/v2 v2.0.7 // indirect
 	github.com/inconshreveable/mousetrap v1.1.0 // indirect
+	github.com/jmespath/go-jmespath v0.4.0 // indirect
+	github.com/jpillora/backoff v1.0.0 // indirect
+	github.com/juju/gnuflag v1.0.0 // indirect
+	github.com/kch42/buzhash v0.0.0-20160816060738-9bdec3dec7c6 // indirect
+	github.com/klauspost/compress v1.17.6 // indirect
+	github.com/klauspost/cpuid/v2 v2.2.6 // indirect
+	github.com/kylelemons/godebug v1.1.0 // indirect
+	github.com/lestrrat-go/strftime v1.0.6 // indirect
 	github.com/lucasb-eyer/go-colorful v1.2.0 // indirect
+	github.com/mattn/go-colorable v0.1.13 // indirect
 	github.com/mattn/go-isatty v0.0.20 // indirect
 	github.com/mattn/go-localereader v0.0.1 // indirect
 	github.com/mattn/go-runewidth v0.0.16 // indirect
 	github.com/microcosm-cc/bluemonday v1.0.27 // indirect
 	github.com/mitchellh/hashstructure/v2 v2.0.2 // indirect
+	github.com/mohae/uvarint v0.0.0-20160208145430-c3f9e62bf2b0 // indirect
 	github.com/muesli/ansi v0.0.0-20230316100256-276c6243b2f6 // indirect
 	github.com/muesli/cancelreader v0.2.2 // indirect
 	github.com/muesli/reflow v0.3.0 // indirect
 	github.com/ncruces/julianday v1.0.0 // indirect
+	github.com/oracle/oci-go-sdk/v65 v65.55.0 // indirect
 	github.com/pelletier/go-toml/v2 v2.2.4 // indirect
-	github.com/pkg/errors v0.8.1 // indirect
+	github.com/pierrec/lz4/v4 v4.1.21 // indirect
+	github.com/pkg/errors v0.9.1 // indirect
+	github.com/pmezard/go-difflib v1.0.0 // indirect
 	github.com/rivo/uniseg v0.4.7 // indirect
 	github.com/sagikazarmark/locafero v0.11.0 // indirect
+	github.com/sergi/go-diff v1.3.1 // indirect
+	github.com/shopspring/decimal v1.3.1 // indirect
+	github.com/silvasur/buzhash v0.0.0-20160816060738-9bdec3dec7c6 // indirect
+	github.com/sirupsen/logrus v1.9.3 // indirect
+	github.com/sony/gobreaker v0.5.0 // indirect
 	github.com/sourcegraph/conc v0.3.1-0.20240121214520-5f936abd7ae8 // indirect
 	github.com/spf13/afero v1.15.0 // indirect
 	github.com/spf13/cast v1.10.0 // indirect
@@ -71,12 +134,40 @@ require (
 	github.com/tidwall/match v1.1.1 // indirect
 	github.com/tidwall/pretty v1.2.1 // indirect
 	github.com/tidwall/sjson v1.2.5 // indirect
+	github.com/vbauerster/mpb/v8 v8.7.2 // indirect
+	github.com/xitongsys/parquet-go v1.6.2 // indirect
+	github.com/xitongsys/parquet-go-source v0.0.0-20240122235623-d6294584ab18 // indirect
 	github.com/xo/terminfo v0.0.0-20220910002029-abceb7e1c41e // indirect
 	github.com/yuin/goldmark v1.7.8 // indirect
 	github.com/yuin/goldmark-emoji v1.0.5 // indirect
+	github.com/zeebo/xxh3 v1.0.2 // indirect
+	go.opencensus.io v0.24.0 // indirect
+	go.opentelemetry.io/contrib/instrumentation/google.golang.org/grpc/otelgrpc v0.49.0 // indirect
+	go.opentelemetry.io/contrib/instrumentation/net/http/otelhttp v0.49.0 // indirect
+	go.opentelemetry.io/otel v1.24.0 // indirect
+	go.opentelemetry.io/otel/metric v1.24.0 // indirect
+	go.opentelemetry.io/otel/trace v1.24.0 // indirect
+	go.uber.org/multierr v1.11.0 // indirect
+	go.uber.org/zap v1.26.0 // indirect
 	go.yaml.in/yaml/v3 v3.0.4 // indirect
+	golang.org/x/crypto v0.46.0 // indirect
+	golang.org/x/exp v0.0.0-20240205201215-2c58cdc269a3 // indirect
 	golang.org/x/net v0.48.0 // indirect
+	golang.org/x/oauth2 v0.30.0 // indirect
 	golang.org/x/sync v0.19.0 // indirect
+	golang.org/x/telemetry v0.0.0-20251203150158-8fff8a5912fc // indirect
 	golang.org/x/text v0.32.0 // indirect
+	golang.org/x/time v0.5.0 // indirect
 	golang.org/x/tools v0.40.0 // indirect
+	golang.org/x/xerrors v0.0.0-20231012003039-104605ab7028 // indirect
+	google.golang.org/api v0.189.0 // indirect
+	google.golang.org/genproto v0.0.0-20240722135656-d784300faade // indirect
+	google.golang.org/genproto/googleapis/api v0.0.0-20240701130421-f6361c86f094 // indirect
+	google.golang.org/genproto/googleapis/rpc v0.0.0-20240722135656-d784300faade // indirect
+	google.golang.org/grpc v1.64.1 // indirect
+	google.golang.org/protobuf v1.34.2 // indirect
+	gopkg.in/errgo.v2 v2.1.0 // indirect
+	gopkg.in/square/go-jose.v2 v2.6.0 // indirect
+	gopkg.in/src-d/go-errors.v1 v1.0.0 // indirect
+	gopkg.in/yaml.v2 v2.4.0 // indirect
 )

internal/storage/dolt/config.go

@@ -0,0 +1,110 @@
+package dolt
+
+import (
+	"context"
+	"database/sql"
+	"fmt"
+	"strings"
+)
+
+// SetConfig sets a configuration value
+func (s *DoltStore) SetConfig(ctx context.Context, key, value string) error {
+	_, err := s.db.ExecContext(ctx, `
+		INSERT INTO config (` + "`key`" + `, value) VALUES (?, ?)
+		ON DUPLICATE KEY UPDATE value = VALUES(value)
+	`, key, value)
+	if err != nil {
+		return fmt.Errorf("failed to set config %s: %w", key, err)
+	}
+	return nil
+}
+
+// GetConfig retrieves a configuration value
+func (s *DoltStore) GetConfig(ctx context.Context, key string) (string, error) {
+	var value string
+	err := s.db.QueryRowContext(ctx, "SELECT value FROM config WHERE `key` = ?", key).Scan(&value)
+	if err == sql.ErrNoRows {
+		return "", nil
+	}
+	if err != nil {
+		return "", fmt.Errorf("failed to get config %s: %w", key, err)
+	}
+	return value, nil
+}
+
+// GetAllConfig retrieves all configuration values
+func (s *DoltStore) GetAllConfig(ctx context.Context) (map[string]string, error) {
+	rows, err := s.db.QueryContext(ctx, "SELECT `key`, value FROM config")
+	if err != nil {
+		return nil, fmt.Errorf("failed to get all config: %w", err)
+	}
+	defer rows.Close()
+
+	config := make(map[string]string)
+	for rows.Next() {
+		var key, value string
+		if err := rows.Scan(&key, &value); err != nil {
+			return nil, fmt.Errorf("failed to scan config: %w", err)
+		}
+		config[key] = value
+	}
+	return config, rows.Err()
+}
+
+// DeleteConfig removes a configuration value
+func (s *DoltStore) DeleteConfig(ctx context.Context, key string) error {
+	_, err := s.db.ExecContext(ctx, "DELETE FROM config WHERE `key` = ?", key)
+	if err != nil {
+		return fmt.Errorf("failed to delete config %s: %w", key, err)
+	}
+	return nil
+}
+
+// SetMetadata sets a metadata value
+func (s *DoltStore) SetMetadata(ctx context.Context, key, value string) error {
+	_, err := s.db.ExecContext(ctx, `
+		INSERT INTO metadata (` + "`key`" + `, value) VALUES (?, ?)
+		ON DUPLICATE KEY UPDATE value = VALUES(value)
+	`, key, value)
+	if err != nil {
+		return fmt.Errorf("failed to set metadata %s: %w", key, err)
+	}
+	return nil
+}
+
+// GetMetadata retrieves a metadata value
+func (s *DoltStore) GetMetadata(ctx context.Context, key string) (string, error) {
+	var value string
+	err := s.db.QueryRowContext(ctx, "SELECT value FROM metadata WHERE `key` = ?", key).Scan(&value)
+	if err == sql.ErrNoRows {
+		return "", nil
+	}
+	if err != nil {
+		return "", fmt.Errorf("failed to get metadata %s: %w", key, err)
+	}
+	return value, nil
+}
+
+// GetCustomStatuses returns custom status values from config
+func (s *DoltStore) GetCustomStatuses(ctx context.Context) ([]string, error) {
+	value, err := s.GetConfig(ctx, "status.custom")
+	if err != nil {
+		return nil, err
+	}
+	if value == "" {
+		return nil, nil
+	}
+	return strings.Split(value, ","), nil
+}
+
+// GetCustomTypes returns custom issue type values from config
+func (s *DoltStore) GetCustomTypes(ctx context.Context) ([]string, error) {
+	value, err := s.GetConfig(ctx, "types.custom")
+	if err != nil {
+		return nil, err
+	}
+	if value == "" {
+		return nil, nil
+	}
+	return strings.Split(value, ","), nil
+}

internal/storage/dolt/dependencies.go

@@ -0,0 +1,496 @@
+package dolt
+
+import (
+	"context"
+	"database/sql"
+	"fmt"
+	"strings"
+
+	"github.com/steveyegge/beads/internal/types"
+)
+
+// AddDependency adds a dependency between two issues
+func (s *DoltStore) AddDependency(ctx context.Context, dep *types.Dependency, actor string) error {
+	metadata := dep.Metadata
+	if metadata == "" {
+		metadata = "{}"
+	}
+
+	_, err := s.db.ExecContext(ctx, `
+		INSERT INTO dependencies (issue_id, depends_on_id, type, created_at, created_by, metadata, thread_id)
+		VALUES (?, ?, ?, NOW(), ?, ?, ?)
+		ON DUPLICATE KEY UPDATE type = VALUES(type), metadata = VALUES(metadata)
+	`, dep.IssueID, dep.DependsOnID, dep.Type, actor, metadata, dep.ThreadID)
+	if err != nil {
+		return fmt.Errorf("failed to add dependency: %w", err)
+	}
+	return nil
+}
+
+// RemoveDependency removes a dependency between two issues
+func (s *DoltStore) RemoveDependency(ctx context.Context, issueID, dependsOnID string, actor string) error {
+	_, err := s.db.ExecContext(ctx, `
+		DELETE FROM dependencies WHERE issue_id = ? AND depends_on_id = ?
+	`, issueID, dependsOnID)
+	if err != nil {
+		return fmt.Errorf("failed to remove dependency: %w", err)
+	}
+	return nil
+}
+
+// GetDependencies retrieves issues that this issue depends on
+func (s *DoltStore) GetDependencies(ctx context.Context, issueID string) ([]*types.Issue, error) {
+	rows, err := s.db.QueryContext(ctx, `
+		SELECT i.id FROM issues i
+		JOIN dependencies d ON i.id = d.depends_on_id
+		WHERE d.issue_id = ?
+		ORDER BY i.priority ASC, i.created_at DESC
+	`, issueID)
+	if err != nil {
+		return nil, fmt.Errorf("failed to get dependencies: %w", err)
+	}
+	defer rows.Close()
+
+	return s.scanIssueIDs(ctx, rows)
+}
+
+// GetDependents retrieves issues that depend on this issue
+func (s *DoltStore) GetDependents(ctx context.Context, issueID string) ([]*types.Issue, error) {
+	rows, err := s.db.QueryContext(ctx, `
+		SELECT i.id FROM issues i
+		JOIN dependencies d ON i.id = d.issue_id
+		WHERE d.depends_on_id = ?
+		ORDER BY i.priority ASC, i.created_at DESC
+	`, issueID)
+	if err != nil {
+		return nil, fmt.Errorf("failed to get dependents: %w", err)
+	}
+	defer rows.Close()
+
+	return s.scanIssueIDs(ctx, rows)
+}
+
+// GetDependenciesWithMetadata returns dependencies with metadata
+func (s *DoltStore) GetDependenciesWithMetadata(ctx context.Context, issueID string) ([]*types.IssueWithDependencyMetadata, error) {
+	rows, err := s.db.QueryContext(ctx, `
+		SELECT d.depends_on_id, d.type, d.created_at, d.created_by, d.metadata, d.thread_id
+		FROM dependencies d
+		WHERE d.issue_id = ?
+	`, issueID)
+	if err != nil {
+		return nil, fmt.Errorf("failed to get dependencies with metadata: %w", err)
+	}
+	defer rows.Close()
+
+	var results []*types.IssueWithDependencyMetadata
+	for rows.Next() {
+		var depID, depType, createdBy string
+		var createdAt sql.NullTime
+		var metadata, threadID sql.NullString
+
+		if err := rows.Scan(&depID, &depType, &createdAt, &createdBy, &metadata, &threadID); err != nil {
+			return nil, fmt.Errorf("failed to scan dependency: %w", err)
+		}
+
+		issue, err := s.GetIssue(ctx, depID)
+		if err != nil {
+			return nil, err
+		}
+		if issue == nil {
+			continue
+		}
+
+		result := &types.IssueWithDependencyMetadata{
+			Issue:          *issue,
+			DependencyType: types.DependencyType(depType),
+		}
+		results = append(results, result)
+	}
+	return results, rows.Err()
+}
+
+// GetDependentsWithMetadata returns dependents with metadata
+func (s *DoltStore) GetDependentsWithMetadata(ctx context.Context, issueID string) ([]*types.IssueWithDependencyMetadata, error) {
+	rows, err := s.db.QueryContext(ctx, `
+		SELECT d.issue_id, d.type, d.created_at, d.created_by, d.metadata, d.thread_id
+		FROM dependencies d
+		WHERE d.depends_on_id = ?
+	`, issueID)
+	if err != nil {
+		return nil, fmt.Errorf("failed to get dependents with metadata: %w", err)
+	}
+	defer rows.Close()
+
+	var results []*types.IssueWithDependencyMetadata
+	for rows.Next() {
+		var depID, depType, createdBy string
+		var createdAt sql.NullTime
+		var metadata, threadID sql.NullString
+
+		if err := rows.Scan(&depID, &depType, &createdAt, &createdBy, &metadata, &threadID); err != nil {
+			return nil, fmt.Errorf("failed to scan dependent: %w", err)
+		}
+
+		issue, err := s.GetIssue(ctx, depID)
+		if err != nil {
+			return nil, err
+		}
+		if issue == nil {
+			continue
+		}
+
+		result := &types.IssueWithDependencyMetadata{
+			Issue:          *issue,
+			DependencyType: types.DependencyType(depType),
+		}
+		results = append(results, result)
+	}
+	return results, rows.Err()
+}
+
+// GetDependencyRecords returns raw dependency records for an issue
+func (s *DoltStore) GetDependencyRecords(ctx context.Context, issueID string) ([]*types.Dependency, error) {
+	rows, err := s.db.QueryContext(ctx, `
+		SELECT issue_id, depends_on_id, type, created_at, created_by, metadata, thread_id
+		FROM dependencies
+		WHERE issue_id = ?
+	`, issueID)
+	if err != nil {
+		return nil, fmt.Errorf("failed to get dependency records: %w", err)
+	}
+	defer rows.Close()
+
+	return scanDependencyRows(rows)
+}
+
+// GetAllDependencyRecords returns all dependency records
+func (s *DoltStore) GetAllDependencyRecords(ctx context.Context) (map[string][]*types.Dependency, error) {
+	rows, err := s.db.QueryContext(ctx, `
+		SELECT issue_id, depends_on_id, type, created_at, created_by, metadata, thread_id
+		FROM dependencies
+		ORDER BY issue_id
+	`)
+	if err != nil {
+		return nil, fmt.Errorf("failed to get all dependency records: %w", err)
+	}
+	defer rows.Close()
+
+	result := make(map[string][]*types.Dependency)
+	for rows.Next() {
+		dep, err := scanDependencyRow(rows)
+		if err != nil {
+			return nil, err
+		}
+		result[dep.IssueID] = append(result[dep.IssueID], dep)
+	}
+	return result, rows.Err()
+}
+
+// GetDependencyCounts returns dependency counts for multiple issues
+func (s *DoltStore) GetDependencyCounts(ctx context.Context, issueIDs []string) (map[string]*types.DependencyCounts, error) {
+	if len(issueIDs) == 0 {
+		return make(map[string]*types.DependencyCounts), nil
+	}
+
+	placeholders := make([]string, len(issueIDs))
+	args := make([]interface{}, len(issueIDs))
+	for i, id := range issueIDs {
+		placeholders[i] = "?"
+		args[i] = id
+	}
+	inClause := strings.Join(placeholders, ",")
+
+	// Query for dependencies (blockers)
+	depQuery := fmt.Sprintf(`
+		SELECT issue_id, COUNT(*) as cnt
+		FROM dependencies
+		WHERE issue_id IN (%s) AND type = 'blocks'
+		GROUP BY issue_id
+	`, inClause)
+
+	depRows, err := s.db.QueryContext(ctx, depQuery, args...)
+	if err != nil {
+		return nil, fmt.Errorf("failed to get dependency counts: %w", err)
+	}
+	defer depRows.Close()
+
+	result := make(map[string]*types.DependencyCounts)
+	for _, id := range issueIDs {
+		result[id] = &types.DependencyCounts{}
+	}
+
+	for depRows.Next() {
+		var id string
+		var cnt int
+		if err := depRows.Scan(&id, &cnt); err != nil {
+			return nil, fmt.Errorf("failed to scan dep count: %w", err)
+		}
+		if c, ok := result[id]; ok {
+			c.DependencyCount = cnt
+		}
+	}
+
+	// Query for dependents (blocking)
+	blockingQuery := fmt.Sprintf(`
+		SELECT depends_on_id, COUNT(*) as cnt
+		FROM dependencies
+		WHERE depends_on_id IN (%s) AND type = 'blocks'
+		GROUP BY depends_on_id
+	`, inClause)
+
+	blockingRows, err := s.db.QueryContext(ctx, blockingQuery, args...)
+	if err != nil {
+		return nil, fmt.Errorf("failed to get blocking counts: %w", err)
+	}
+	defer blockingRows.Close()
+
+	for blockingRows.Next() {
+		var id string
+		var cnt int
+		if err := blockingRows.Scan(&id, &cnt); err != nil {
+			return nil, fmt.Errorf("failed to scan blocking count: %w", err)
+		}
+		if c, ok := result[id]; ok {
+			c.DependentCount = cnt
+		}
+	}
+
+	return result, nil
+}
+
+// GetDependencyTree returns a dependency tree for visualization
+func (s *DoltStore) GetDependencyTree(ctx context.Context, issueID string, maxDepth int, showAllPaths bool, reverse bool) ([]*types.TreeNode, error) {
+	// Simple implementation - can be optimized with CTE
+	visited := make(map[string]bool)
+	return s.buildDependencyTree(ctx, issueID, 0, maxDepth, reverse, visited)
+}
+
+func (s *DoltStore) buildDependencyTree(ctx context.Context, issueID string, depth, maxDepth int, reverse bool, visited map[string]bool) ([]*types.TreeNode, error) {
+	if depth >= maxDepth || visited[issueID] {
+		return nil, nil
+	}
+	visited[issueID] = true
+
+	issue, err := s.GetIssue(ctx, issueID)
+	if err != nil || issue == nil {
+		return nil, err
+	}
+
+	var childIDs []string
+	var query string
+	if reverse {
+		query = "SELECT issue_id FROM dependencies WHERE depends_on_id = ?"
+	} else {
+		query = "SELECT depends_on_id FROM dependencies WHERE issue_id = ?"
+	}
+
+	rows, err := s.db.QueryContext(ctx, query, issueID)
+	if err != nil {
+		return nil, err
+	}
+	defer rows.Close()
+
+	for rows.Next() {
+		var id string
+		if err := rows.Scan(&id); err != nil {
+			return nil, err
+		}
+		childIDs = append(childIDs, id)
+	}
+
+	node := &types.TreeNode{
+		Issue: *issue,
+		Depth: depth,
+	}
+
+	// TreeNode doesn't have Children field - return flat list
+	nodes := []*types.TreeNode{node}
+	for _, childID := range childIDs {
+		children, err := s.buildDependencyTree(ctx, childID, depth+1, maxDepth, reverse, visited)
+		if err != nil {
+			return nil, err
+		}
+		nodes = append(nodes, children...)
+	}
+
+	return nodes, nil
+}
+
+// DetectCycles finds circular dependencies
+func (s *DoltStore) DetectCycles(ctx context.Context) ([][]*types.Issue, error) {
+	// Get all dependencies
+	deps, err := s.GetAllDependencyRecords(ctx)
+	if err != nil {
+		return nil, err
+	}
+
+	// Build adjacency list
+	graph := make(map[string][]string)
+	for issueID, records := range deps {
+		for _, dep := range records {
+			if dep.Type == types.DepBlocks {
+				graph[issueID] = append(graph[issueID], dep.DependsOnID)
+			}
+		}
+	}
+
+	// Find cycles using DFS
+	var cycles [][]*types.Issue
+	visited := make(map[string]bool)
+	recStack := make(map[string]bool)
+	path := make([]string, 0)
+
+	var dfs func(node string) bool
+	dfs = func(node string) bool {
+		visited[node] = true
+		recStack[node] = true
+		path = append(path, node)
+
+		for _, neighbor := range graph[node] {
+			if !visited[neighbor] {
+				if dfs(neighbor) {
+					return true
+				}
+			} else if recStack[neighbor] {
+				// Found cycle - extract it
+				cycleStart := -1
+				for i, n := range path {
+					if n == neighbor {
+						cycleStart = i
+						break
+					}
+				}
+				if cycleStart >= 0 {
+					cyclePath := path[cycleStart:]
+					var cycleIssues []*types.Issue
+					for _, id := range cyclePath {
+						issue, _ := s.GetIssue(ctx, id)
+						if issue != nil {
+							cycleIssues = append(cycleIssues, issue)
+						}
+					}
+					if len(cycleIssues) > 0 {
+						cycles = append(cycles, cycleIssues)
+					}
+				}
+			}
+		}
+
+		path = path[:len(path)-1]
+		recStack[node] = false
+		return false
+	}
+
+	for node := range graph {
+		if !visited[node] {
+			dfs(node)
+		}
+	}
+
+	return cycles, nil
+}
+
+// IsBlocked checks if an issue has open blockers
+func (s *DoltStore) IsBlocked(ctx context.Context, issueID string) (bool, []string, error) {
+	rows, err := s.db.QueryContext(ctx, `
+		SELECT d.depends_on_id
+		FROM dependencies d
+		JOIN issues i ON d.depends_on_id = i.id
+		WHERE d.issue_id = ?
+		  AND d.type = 'blocks'
+		  AND i.status IN ('open', 'in_progress', 'blocked', 'deferred', 'hooked')
+	`, issueID)
+	if err != nil {
+		return false, nil, fmt.Errorf("failed to check blockers: %w", err)
+	}
+	defer rows.Close()
+
+	var blockers []string
+	for rows.Next() {
+		var id string
+		if err := rows.Scan(&id); err != nil {
+			return false, nil, err
+		}
+		blockers = append(blockers, id)
+	}
+
+	return len(blockers) > 0, blockers, rows.Err()
+}
+
+// GetNewlyUnblockedByClose finds issues that become unblocked when an issue is closed
+func (s *DoltStore) GetNewlyUnblockedByClose(ctx context.Context, closedIssueID string) ([]*types.Issue, error) {
+	// Find issues that were blocked only by the closed issue
+	rows, err := s.db.QueryContext(ctx, `
+		SELECT DISTINCT d.issue_id
+		FROM dependencies d
+		JOIN issues i ON d.issue_id = i.id
+		WHERE d.depends_on_id = ?
+		  AND d.type = 'blocks'
+		  AND i.status IN ('open', 'blocked')
+		  AND NOT EXISTS (
+			SELECT 1 FROM dependencies d2
+			JOIN issues blocker ON d2.depends_on_id = blocker.id
+			WHERE d2.issue_id = d.issue_id
+			  AND d2.type = 'blocks'
+			  AND d2.depends_on_id != ?
+			  AND blocker.status IN ('open', 'in_progress', 'blocked', 'deferred', 'hooked')
+		  )
+	`, closedIssueID, closedIssueID)
+	if err != nil {
+		return nil, fmt.Errorf("failed to find newly unblocked: %w", err)
+	}
+	defer rows.Close()
+
+	return s.scanIssueIDs(ctx, rows)
+}
+
+// Helper functions
+
+func (s *DoltStore) scanIssueIDs(ctx context.Context, rows *sql.Rows) ([]*types.Issue, error) {
+	var issues []*types.Issue
+	for rows.Next() {
+		var id string
+		if err := rows.Scan(&id); err != nil {
+			return nil, fmt.Errorf("failed to scan issue id: %w", err)
+		}
+		issue, err := s.GetIssue(ctx, id)
+		if err != nil {
+			return nil, err
+		}
+		if issue != nil {
+			issues = append(issues, issue)
+		}
+	}
+	return issues, rows.Err()
+}
+
+func scanDependencyRows(rows *sql.Rows) ([]*types.Dependency, error) {
+	var deps []*types.Dependency
+	for rows.Next() {
+		dep, err := scanDependencyRow(rows)
+		if err != nil {
+			return nil, err
+		}
+		deps = append(deps, dep)
+	}
+	return deps, rows.Err()
+}
+
+func scanDependencyRow(rows *sql.Rows) (*types.Dependency, error) {
+	var dep types.Dependency
+	var createdAt sql.NullTime
+	var metadata, threadID sql.NullString
+
+	if err := rows.Scan(&dep.IssueID, &dep.DependsOnID, &dep.Type, &createdAt, &dep.CreatedBy, &metadata, &threadID); err != nil {
+		return nil, fmt.Errorf("failed to scan dependency: %w", err)
+	}
+
+	if createdAt.Valid {
+		dep.CreatedAt = createdAt.Time
+	}
+	if threadID.Valid {
+		dep.ThreadID = threadID.String
+	}
+
+	return &dep, nil
+}

internal/storage/dolt/dirty.go

@@ -0,0 +1,108 @@
+package dolt
+
+import (
+	"context"
+	"fmt"
+	"strings"
+	"time"
+)
+
+// GetDirtyIssues returns IDs of issues that have been modified since last export
+func (s *DoltStore) GetDirtyIssues(ctx context.Context) ([]string, error) {
+	rows, err := s.db.QueryContext(ctx, `
+		SELECT issue_id FROM dirty_issues ORDER BY marked_at ASC
+	`)
+	if err != nil {
+		return nil, fmt.Errorf("failed to get dirty issues: %w", err)
+	}
+	defer rows.Close()
+
+	var ids []string
+	for rows.Next() {
+		var id string
+		if err := rows.Scan(&id); err != nil {
+			return nil, fmt.Errorf("failed to scan issue id: %w", err)
+		}
+		ids = append(ids, id)
+	}
+	return ids, rows.Err()
+}
+
+// GetDirtyIssueHash returns the dirty hash for a specific issue
+func (s *DoltStore) GetDirtyIssueHash(ctx context.Context, issueID string) (string, error) {
+	var hash string
+	err := s.db.QueryRowContext(ctx, `
+		SELECT i.content_hash FROM issues i
+		JOIN dirty_issues d ON i.id = d.issue_id
+		WHERE d.issue_id = ?
+	`, issueID).Scan(&hash)
+	if err != nil {
+		return "", fmt.Errorf("failed to get dirty issue hash: %w", err)
+	}
+	return hash, nil
+}
+
+// ClearDirtyIssuesByID removes specific issues from the dirty list
+func (s *DoltStore) ClearDirtyIssuesByID(ctx context.Context, issueIDs []string) error {
+	if len(issueIDs) == 0 {
+		return nil
+	}
+
+	placeholders := make([]string, len(issueIDs))
+	args := make([]interface{}, len(issueIDs))
+	for i, id := range issueIDs {
+		placeholders[i] = "?"
+		args[i] = id
+	}
+
+	query := fmt.Sprintf("DELETE FROM dirty_issues WHERE issue_id IN (%s)", strings.Join(placeholders, ","))
+	_, err := s.db.ExecContext(ctx, query, args...)
+	if err != nil {
+		return fmt.Errorf("failed to clear dirty issues: %w", err)
+	}
+	return nil
+}
+
+// GetExportHash returns the last export hash for an issue
+func (s *DoltStore) GetExportHash(ctx context.Context, issueID string) (string, error) {
+	var hash string
+	err := s.db.QueryRowContext(ctx, `
+		SELECT content_hash FROM export_hashes WHERE issue_id = ?
+	`, issueID).Scan(&hash)
+	if err != nil {
+		return "", nil // Not found is OK
+	}
+	return hash, nil
+}
+
+// SetExportHash stores the export hash for an issue
+func (s *DoltStore) SetExportHash(ctx context.Context, issueID, contentHash string) error {
+	_, err := s.db.ExecContext(ctx, `
+		INSERT INTO export_hashes (issue_id, content_hash, exported_at)
+		VALUES (?, ?, ?)
+		ON DUPLICATE KEY UPDATE content_hash = VALUES(content_hash), exported_at = VALUES(exported_at)
+	`, issueID, contentHash, time.Now())
+	if err != nil {
+		return fmt.Errorf("failed to set export hash: %w", err)
+	}
+	return nil
+}
+
+// ClearAllExportHashes removes all export hashes (for full re-export)
+func (s *DoltStore) ClearAllExportHashes(ctx context.Context) error {
+	_, err := s.db.ExecContext(ctx, "DELETE FROM export_hashes")
+	if err != nil {
+		return fmt.Errorf("failed to clear export hashes: %w", err)
+	}
+	return nil
+}
+
+// GetJSONLFileHash returns the stored JSONL file hash
+func (s *DoltStore) GetJSONLFileHash(ctx context.Context) (string, error) {
+	return s.GetMetadata(ctx, "jsonl_file_hash")
+}
+
+// SetJSONLFileHash stores the JSONL file hash
+func (s *DoltStore) SetJSONLFileHash(ctx context.Context, fileHash string) error {
+	return s.SetMetadata(ctx, "jsonl_file_hash", fileHash)
+}

internal/storage/dolt/dolt_test.go

@@ -0,0 +1,853 @@
+package dolt
+
+import (
+	"context"
+	"os"
+	"testing"
+
+	"github.com/steveyegge/beads/internal/types"
+)
+
+// skipIfNoDolt skips the test if Dolt is not installed
+func skipIfNoDolt(t *testing.T) {
+	t.Helper()
+	if _, err := os.Stat("/usr/local/bin/dolt"); os.IsNotExist(err) {
+		t.Skip("Dolt not installed, skipping test")
+	}
+}
+
+// setupTestStore creates a test store with a temporary directory
+func setupTestStore(t *testing.T) (*DoltStore, func()) {
+	t.Helper()
+	skipIfNoDolt(t)
+
+	ctx := context.Background()
+	tmpDir, err := os.MkdirTemp("", "dolt-test-*")
+	if err != nil {
+		t.Fatalf("failed to create temp dir: %v", err)
+	}
+
+	cfg := &Config{
+		Path:           tmpDir,
+		CommitterName:  "test",
+		CommitterEmail: "test@example.com",
+		Database:       "testdb",
+	}
+
+	store, err := New(ctx, cfg)
+	if err != nil {
+		os.RemoveAll(tmpDir)
+		t.Fatalf("failed to create Dolt store: %v", err)
+	}
+
+	// Set up issue prefix
+	if err := store.SetConfig(ctx, "issue_prefix", "test"); err != nil {
+		store.Close()
+		os.RemoveAll(tmpDir)
+		t.Fatalf("failed to set prefix: %v", err)
+	}
+
+	cleanup := func() {
+		store.Close()
+		os.RemoveAll(tmpDir)
+	}
+
+	return store, cleanup
+}
+
+func TestNewDoltStore(t *testing.T) {
+	skipIfNoDolt(t)
+
+	ctx := context.Background()
+	tmpDir, err := os.MkdirTemp("", "dolt-test-*")
+	if err != nil {
+		t.Fatalf("failed to create temp dir: %v", err)
+	}
+	defer os.RemoveAll(tmpDir)
+
+	cfg := &Config{
+		Path:           tmpDir,
+		CommitterName:  "test",
+		CommitterEmail: "test@example.com",
+		Database:       "testdb",
+	}
+
+	store, err := New(ctx, cfg)
+	if err != nil {
+		t.Fatalf("failed to create Dolt store: %v", err)
+	}
+	defer store.Close()
+
+	// Verify store path
+	if store.Path() != tmpDir {
+		t.Errorf("expected path %s, got %s", tmpDir, store.Path())
+	}
+
+	// Verify not closed
+	if store.IsClosed() {
+		t.Error("store should not be closed")
+	}
+}
+
+func TestDoltStoreConfig(t *testing.T) {
+	store, cleanup := setupTestStore(t)
+	defer cleanup()
+
+	ctx := context.Background()
+
+	// Test SetConfig
+	if err := store.SetConfig(ctx, "test_key", "test_value"); err != nil {
+		t.Fatalf("failed to set config: %v", err)
+	}
+
+	// Test GetConfig
+	value, err := store.GetConfig(ctx, "test_key")
+	if err != nil {
+		t.Fatalf("failed to get config: %v", err)
+	}
+	if value != "test_value" {
+		t.Errorf("expected 'test_value', got %q", value)
+	}
+
+	// Test GetAllConfig
+	allConfig, err := store.GetAllConfig(ctx)
+	if err != nil {
+		t.Fatalf("failed to get all config: %v", err)
+	}
+	if allConfig["test_key"] != "test_value" {
+		t.Errorf("expected test_key in all config")
+	}
+
+	// Test DeleteConfig
+	if err := store.DeleteConfig(ctx, "test_key"); err != nil {
+		t.Fatalf("failed to delete config: %v", err)
+	}
+	value, err = store.GetConfig(ctx, "test_key")
+	if err != nil {
+		t.Fatalf("failed to get deleted config: %v", err)
+	}
+	if value != "" {
+		t.Errorf("expected empty value after delete, got %q", value)
+	}
+}
+
+func TestDoltStoreIssue(t *testing.T) {
+	store, cleanup := setupTestStore(t)
+	defer cleanup()
+
+	ctx := context.Background()
+
+	// Create an issue
+	issue := &types.Issue{
+		Title:       "Test Issue",
+		Description: "Test description",
+		Status:      types.StatusOpen,
+		Priority:    2,
+		IssueType:   types.TypeTask,
+	}
+
+	if err := store.CreateIssue(ctx, issue, "tester"); err != nil {
+		t.Fatalf("failed to create issue: %v", err)
+	}
+
+	// Verify ID was generated
+	if issue.ID == "" {
+		t.Error("expected issue ID to be generated")
+	}
+
+	// Get the issue back
+	retrieved, err := store.GetIssue(ctx, issue.ID)
+	if err != nil {
+		t.Fatalf("failed to get issue: %v", err)
+	}
+	if retrieved == nil {
+		t.Fatal("expected to retrieve issue")
+	}
+	if retrieved.Title != issue.Title {
+		t.Errorf("expected title %q, got %q", issue.Title, retrieved.Title)
+	}
+}
+
+func TestDoltStoreIssueUpdate(t *testing.T) {
+	store, cleanup := setupTestStore(t)
+	defer cleanup()
+
+	ctx := context.Background()
+
+	// Create an issue
+	issue := &types.Issue{
+		Title:       "Original Title",
+		Description: "Original description",
+		Status:      types.StatusOpen,
+		Priority:    2,
+		IssueType:   types.TypeTask,
+	}
+
+	if err := store.CreateIssue(ctx, issue, "tester"); err != nil {
+		t.Fatalf("failed to create issue: %v", err)
+	}
+
+	// Update the issue
+	updates := map[string]interface{}{
+		"title":    "Updated Title",
+		"priority": 1,
+		"status":   string(types.StatusInProgress),
+	}
+
+	if err := store.UpdateIssue(ctx, issue.ID, updates, "tester"); err != nil {
+		t.Fatalf("failed to update issue: %v", err)
+	}
+
+	// Get the updated issue
+	retrieved, err := store.GetIssue(ctx, issue.ID)
+	if err != nil {
+		t.Fatalf("failed to get issue: %v", err)
+	}
+	if retrieved.Title != "Updated Title" {
+		t.Errorf("expected title 'Updated Title', got %q", retrieved.Title)
+	}
+	if retrieved.Priority != 1 {
+		t.Errorf("expected priority 1, got %d", retrieved.Priority)
+	}
+	if retrieved.Status != types.StatusInProgress {
+		t.Errorf("expected status in_progress, got %s", retrieved.Status)
+	}
+}
+
+func TestDoltStoreIssueClose(t *testing.T) {
+	store, cleanup := setupTestStore(t)
+	defer cleanup()
+
+	ctx := context.Background()
+
+	// Create an issue
+	issue := &types.Issue{
+		Title:       "Issue to Close",
+		Description: "Will be closed",
+		Status:      types.StatusOpen,
+		Priority:    2,
+		IssueType:   types.TypeTask,
+	}
+
+	if err := store.CreateIssue(ctx, issue, "tester"); err != nil {
+		t.Fatalf("failed to create issue: %v", err)
+	}
+
+	// Close the issue
+	if err := store.CloseIssue(ctx, issue.ID, "completed", "tester", "session123"); err != nil {
+		t.Fatalf("failed to close issue: %v", err)
+	}
+
+	// Get the closed issue
+	retrieved, err := store.GetIssue(ctx, issue.ID)
+	if err != nil {
+		t.Fatalf("failed to get issue: %v", err)
+	}
+	if retrieved.Status != types.StatusClosed {
+		t.Errorf("expected status closed, got %s", retrieved.Status)
+	}
+	if retrieved.ClosedAt == nil {
+		t.Error("expected closed_at to be set")
+	}
+}
+
+func TestDoltStoreLabels(t *testing.T) {
+	store, cleanup := setupTestStore(t)
+	defer cleanup()
+
+	ctx := context.Background()
+
+	// Create an issue
+	issue := &types.Issue{
+		Title:       "Issue with Labels",
+		Description: "Test labels",
+		Status:      types.StatusOpen,
+		Priority:    2,
+		IssueType:   types.TypeTask,
+	}
+
+	if err := store.CreateIssue(ctx, issue, "tester"); err != nil {
+		t.Fatalf("failed to create issue: %v", err)
+	}
+
+	// Add labels
+	if err := store.AddLabel(ctx, issue.ID, "bug", "tester"); err != nil {
+		t.Fatalf("failed to add label: %v", err)
+	}
+	if err := store.AddLabel(ctx, issue.ID, "priority", "tester"); err != nil {
+		t.Fatalf("failed to add second label: %v", err)
+	}
+
+	// Get labels
+	labels, err := store.GetLabels(ctx, issue.ID)
+	if err != nil {
+		t.Fatalf("failed to get labels: %v", err)
+	}
+	if len(labels) != 2 {
+		t.Errorf("expected 2 labels, got %d", len(labels))
+	}
+
+	// Remove label
+	if err := store.RemoveLabel(ctx, issue.ID, "bug", "tester"); err != nil {
+		t.Fatalf("failed to remove label: %v", err)
+	}
+
+	// Verify removal
+	labels, err = store.GetLabels(ctx, issue.ID)
+	if err != nil {
+		t.Fatalf("failed to get labels after removal: %v", err)
+	}
+	if len(labels) != 1 {
+		t.Errorf("expected 1 label after removal, got %d", len(labels))
+	}
+}
+
+func TestDoltStoreDependencies(t *testing.T) {
+	store, cleanup := setupTestStore(t)
+	defer cleanup()
+
+	ctx := context.Background()
+
+	// Create parent and child issues
+	parent := &types.Issue{
+		ID:          "test-parent",
+		Title:       "Parent Issue",
+		Description: "Parent description",
+		Status:      types.StatusOpen,
+		Priority:    1,
+		IssueType:   types.TypeEpic,
+	}
+	child := &types.Issue{
+		ID:          "test-child",
+		Title:       "Child Issue",
+		Description: "Child description",
+		Status:      types.StatusOpen,
+		Priority:    2,
+		IssueType:   types.TypeTask,
+	}
+
+	if err := store.CreateIssue(ctx, parent, "tester"); err != nil {
+		t.Fatalf("failed to create parent issue: %v", err)
+	}
+	if err := store.CreateIssue(ctx, child, "tester"); err != nil {
+		t.Fatalf("failed to create child issue: %v", err)
+	}
+
+	// Add dependency (child depends on parent)
+	dep := &types.Dependency{
+		IssueID:     child.ID,
+		DependsOnID: parent.ID,
+		Type:        types.DepBlocks,
+	}
+	if err := store.AddDependency(ctx, dep, "tester"); err != nil {
+		t.Fatalf("failed to add dependency: %v", err)
+	}
+
+	// Get dependencies
+	deps, err := store.GetDependencies(ctx, child.ID)
+	if err != nil {
+		t.Fatalf("failed to get dependencies: %v", err)
+	}
+	if len(deps) != 1 {
+		t.Errorf("expected 1 dependency, got %d", len(deps))
+	}
+	if deps[0].ID != parent.ID {
+		t.Errorf("expected dependency on %s, got %s", parent.ID, deps[0].ID)
+	}
+
+	// Get dependents
+	dependents, err := store.GetDependents(ctx, parent.ID)
+	if err != nil {
+		t.Fatalf("failed to get dependents: %v", err)
+	}
+	if len(dependents) != 1 {
+		t.Errorf("expected 1 dependent, got %d", len(dependents))
+	}
+
+	// Check if blocked
+	blocked, blockers, err := store.IsBlocked(ctx, child.ID)
+	if err != nil {
+		t.Fatalf("failed to check if blocked: %v", err)
+	}
+	if !blocked {
+		t.Error("expected child to be blocked")
+	}
+	if len(blockers) != 1 || blockers[0] != parent.ID {
+		t.Errorf("expected blocker %s, got %v", parent.ID, blockers)
+	}
+
+	// Remove dependency
+	if err := store.RemoveDependency(ctx, child.ID, parent.ID, "tester"); err != nil {
+		t.Fatalf("failed to remove dependency: %v", err)
+	}
+
+	// Verify removal
+	deps, err = store.GetDependencies(ctx, child.ID)
+	if err != nil {
+		t.Fatalf("failed to get dependencies after removal: %v", err)
+	}
+	if len(deps) != 0 {
+		t.Errorf("expected 0 dependencies after removal, got %d", len(deps))
+	}
+}
+
+func TestDoltStoreSearch(t *testing.T) {
+	store, cleanup := setupTestStore(t)
+	defer cleanup()
+
+	ctx := context.Background()
+
+	// Create multiple issues
+	issues := []*types.Issue{
+		{
+			ID:          "test-search-1",
+			Title:       "First Issue",
+			Description: "Search test one",
+			Status:      types.StatusOpen,
+			Priority:    1,
+			IssueType:   types.TypeTask,
+		},
+		{
+			ID:          "test-search-2",
+			Title:       "Second Issue",
+			Description: "Search test two",
+			Status:      types.StatusOpen,
+			Priority:    2,
+			IssueType:   types.TypeBug,
+		},
+		{
+			ID:          "test-search-3",
+			Title:       "Third Issue",
+			Description: "Different content",
+			Status:      types.StatusClosed,
+			Priority:    3,
+			IssueType:   types.TypeTask,
+		},
+	}
+
+	for _, issue := range issues {
+		if err := store.CreateIssue(ctx, issue, "tester"); err != nil {
+			t.Fatalf("failed to create issue %s: %v", issue.ID, err)
+		}
+	}
+
+	// Search by query
+	results, err := store.SearchIssues(ctx, "Search test", types.IssueFilter{})
+	if err != nil {
+		t.Fatalf("failed to search issues: %v", err)
+	}
+	if len(results) != 2 {
+		t.Errorf("expected 2 results for 'Search test', got %d", len(results))
+	}
+
+	// Search with status filter
+	openStatus := types.StatusOpen
+	results, err = store.SearchIssues(ctx, "", types.IssueFilter{Status: &openStatus})
+	if err != nil {
+		t.Fatalf("failed to search with status filter: %v", err)
+	}
+	if len(results) != 2 {
+		t.Errorf("expected 2 open issues, got %d", len(results))
+	}
+
+	// Search by issue type
+	bugType := types.TypeBug
+	results, err = store.SearchIssues(ctx, "", types.IssueFilter{IssueType: &bugType})
+	if err != nil {
+		t.Fatalf("failed to search by type: %v", err)
+	}
+	if len(results) != 1 {
+		t.Errorf("expected 1 bug, got %d", len(results))
+	}
+}
+
+func TestDoltStoreCreateIssues(t *testing.T) {
+	store, cleanup := setupTestStore(t)
+	defer cleanup()
+
+	ctx := context.Background()
+
+	// Create multiple issues in batch
+	issues := []*types.Issue{
+		{
+			ID:          "test-batch-1",
+			Title:       "Batch Issue 1",
+			Description: "First batch issue",
+			Status:      types.StatusOpen,
+			Priority:    1,
+			IssueType:   types.TypeTask,
+		},
+		{
+			ID:          "test-batch-2",
+			Title:       "Batch Issue 2",
+			Description: "Second batch issue",
+			Status:      types.StatusOpen,
+			Priority:    2,
+			IssueType:   types.TypeTask,
+		},
+	}
+
+	if err := store.CreateIssues(ctx, issues, "tester"); err != nil {
+		t.Fatalf("failed to create issues: %v", err)
+	}
+
+	// Verify all issues were created
+	for _, issue := range issues {
+		retrieved, err := store.GetIssue(ctx, issue.ID)
+		if err != nil {
+			t.Fatalf("failed to get issue %s: %v", issue.ID, err)
+		}
+		if retrieved == nil {
+			t.Errorf("expected to retrieve issue %s", issue.ID)
+		}
+		if retrieved.Title != issue.Title {
+			t.Errorf("expected title %q, got %q", issue.Title, retrieved.Title)
+		}
+	}
+}
+
+func TestDoltStoreComments(t *testing.T) {
+	store, cleanup := setupTestStore(t)
+	defer cleanup()
+
+	ctx := context.Background()
+
+	// Create an issue
+	issue := &types.Issue{
+		ID:          "test-comment-issue",
+		Title:       "Issue with Comments",
+		Description: "Test comments",
+		Status:      types.StatusOpen,
+		Priority:    2,
+		IssueType:   types.TypeTask,
+	}
+
+	if err := store.CreateIssue(ctx, issue, "tester"); err != nil {
+		t.Fatalf("failed to create issue: %v", err)
+	}
+
+	// Add comments
+	comment1, err := store.AddIssueComment(ctx, issue.ID, "user1", "First comment")
+	if err != nil {
+		t.Fatalf("failed to add first comment: %v", err)
+	}
+	if comment1.ID == 0 {
+		t.Error("expected comment ID to be generated")
+	}
+
+	_, err = store.AddIssueComment(ctx, issue.ID, "user2", "Second comment")
+	if err != nil {
+		t.Fatalf("failed to add second comment: %v", err)
+	}
+
+	// Get comments
+	comments, err := store.GetIssueComments(ctx, issue.ID)
+	if err != nil {
+		t.Fatalf("failed to get comments: %v", err)
+	}
+	if len(comments) != 2 {
+		t.Errorf("expected 2 comments, got %d", len(comments))
+	}
+	if comments[0].Text != "First comment" {
+		t.Errorf("expected 'First comment', got %q", comments[0].Text)
+	}
+}
+
+func TestDoltStoreEvents(t *testing.T) {
+	store, cleanup := setupTestStore(t)
+	defer cleanup()
+
+	ctx := context.Background()
+
+	// Create an issue (this creates a creation event)
+	issue := &types.Issue{
+		ID:          "test-event-issue",
+		Title:       "Issue with Events",
+		Description: "Test events",
+		Status:      types.StatusOpen,
+		Priority:    2,
+		IssueType:   types.TypeTask,
+	}
+
+	if err := store.CreateIssue(ctx, issue, "tester"); err != nil {
+		t.Fatalf("failed to create issue: %v", err)
+	}
+
+	// Add a comment event
+	if err := store.AddComment(ctx, issue.ID, "user1", "A comment"); err != nil {
+		t.Fatalf("failed to add comment: %v", err)
+	}
+
+	// Get events
+	events, err := store.GetEvents(ctx, issue.ID, 10)
+	if err != nil {
+		t.Fatalf("failed to get events: %v", err)
+	}
+	if len(events) < 2 {
+		t.Errorf("expected at least 2 events, got %d", len(events))
+	}
+}
+
+func TestDoltStoreDeleteIssue(t *testing.T) {
+	store, cleanup := setupTestStore(t)
+	defer cleanup()
+
+	ctx := context.Background()
+
+	// Create an issue
+	issue := &types.Issue{
+		ID:          "test-delete-issue",
+		Title:       "Issue to Delete",
+		Description: "Will be deleted",
+		Status:      types.StatusOpen,
+		Priority:    2,
+		IssueType:   types.TypeTask,
+	}
+
+	if err := store.CreateIssue(ctx, issue, "tester"); err != nil {
+		t.Fatalf("failed to create issue: %v", err)
+	}
+
+	// Verify it exists
+	retrieved, err := store.GetIssue(ctx, issue.ID)
+	if err != nil || retrieved == nil {
+		t.Fatalf("issue should exist before delete")
+	}
+
+	// Delete the issue
+	if err := store.DeleteIssue(ctx, issue.ID); err != nil {
+		t.Fatalf("failed to delete issue: %v", err)
+	}
+
+	// Verify it's gone
+	retrieved, err = store.GetIssue(ctx, issue.ID)
+	if err != nil {
+		t.Fatalf("failed to get issue after delete: %v", err)
+	}
+	if retrieved != nil {
+		t.Error("expected issue to be deleted")
+	}
+}
+
+func TestDoltStoreDirtyTracking(t *testing.T) {
+	store, cleanup := setupTestStore(t)
+	defer cleanup()
+
+	ctx := context.Background()
+
+	// Create an issue (marks it dirty)
+	issue := &types.Issue{
+		ID:          "test-dirty-issue",
+		Title:       "Dirty Issue",
+		Description: "Will be dirty",
+		Status:      types.StatusOpen,
+		Priority:    2,
+		IssueType:   types.TypeTask,
+	}
+
+	if err := store.CreateIssue(ctx, issue, "tester"); err != nil {
+		t.Fatalf("failed to create issue: %v", err)
+	}
+
+	// Get dirty issues
+	dirtyIDs, err := store.GetDirtyIssues(ctx)
+	if err != nil {
+		t.Fatalf("failed to get dirty issues: %v", err)
+	}
+	found := false
+	for _, id := range dirtyIDs {
+		if id == issue.ID {
+			found = true
+			break
+		}
+	}
+	if !found {
+		t.Error("expected issue to be in dirty list")
+	}
+
+	// Clear dirty issues
+	if err := store.ClearDirtyIssuesByID(ctx, []string{issue.ID}); err != nil {
+		t.Fatalf("failed to clear dirty issues: %v", err)
+	}
+
+	// Verify it's cleared
+	dirtyIDs, err = store.GetDirtyIssues(ctx)
+	if err != nil {
+		t.Fatalf("failed to get dirty issues after clear: %v", err)
+	}
+	for _, id := range dirtyIDs {
+		if id == issue.ID {
+			t.Error("expected issue to be cleared from dirty list")
+		}
+	}
+}
+
+func TestDoltStoreStatistics(t *testing.T) {
+	store, cleanup := setupTestStore(t)
+	defer cleanup()
+
+	ctx := context.Background()
+
+	// Create some issues
+	issues := []*types.Issue{
+		{ID: "test-stat-1", Title: "Open 1", Status: types.StatusOpen, Priority: 1, IssueType: types.TypeTask},
+		{ID: "test-stat-2", Title: "Open 2", Status: types.StatusOpen, Priority: 2, IssueType: types.TypeTask},
+		{ID: "test-stat-3", Title: "Closed", Status: types.StatusClosed, Priority: 1, IssueType: types.TypeTask},
+	}
+
+	for _, issue := range issues {
+		if err := store.CreateIssue(ctx, issue, "tester"); err != nil {
+			t.Fatalf("failed to create issue: %v", err)
+		}
+	}
+
+	// Get statistics
+	stats, err := store.GetStatistics(ctx)
+	if err != nil {
+		t.Fatalf("failed to get statistics: %v", err)
+	}
+
+	if stats.OpenIssues < 2 {
+		t.Errorf("expected at least 2 open issues, got %d", stats.OpenIssues)
+	}
+	if stats.ClosedIssues < 1 {
+		t.Errorf("expected at least 1 closed issue, got %d", stats.ClosedIssues)
+	}
+}
+
+// Test SQL injection protection
+
+func TestValidateRef(t *testing.T) {
+	tests := []struct {
+		name    string
+		ref     string
+		wantErr bool
+	}{
+		{"valid hash", "abc123def456", false},
+		{"valid branch", "main", false},
+		{"valid with underscore", "feature_branch", false},
+		{"valid with dash", "feature-branch", false},
+		{"empty", "", true},
+		{"too long", string(make([]byte, 200)), true},
+		{"with SQL injection", "main'; DROP TABLE issues; --", true},
+		{"with quotes", "main'test", true},
+		{"with semicolon", "main;test", true},
+		{"with space", "main test", true},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			err := validateRef(tt.ref)
+			if (err != nil) != tt.wantErr {
+				t.Errorf("validateRef(%q) error = %v, wantErr %v", tt.ref, err, tt.wantErr)
+			}
+		})
+	}
+}
+
+func TestValidateTableName(t *testing.T) {
+	tests := []struct {
+		name      string
+		tableName string
+		wantErr   bool
+	}{
+		{"valid table", "issues", false},
+		{"valid with underscore", "dirty_issues", false},
+		{"valid with numbers", "table123", false},
+		{"empty", "", true},
+		{"too long", string(make([]byte, 100)), true},
+		{"starts with number", "123table", true},
+		{"with SQL injection", "issues'; DROP TABLE issues; --", true},
+		{"with space", "my table", true},
+		{"with dash", "my-table", true},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			err := validateTableName(tt.tableName)
+			if (err != nil) != tt.wantErr {
+				t.Errorf("validateTableName(%q) error = %v, wantErr %v", tt.tableName, err, tt.wantErr)
+			}
+		})
+	}
+}
+
+func TestDoltStoreGetReadyWork(t *testing.T) {
+	store, cleanup := setupTestStore(t)
+	defer cleanup()
+
+	ctx := context.Background()
+
+	// Create issues: one blocked, one ready
+	blocker := &types.Issue{
+		ID:          "test-blocker",
+		Title:       "Blocker",
+		Description: "Blocks another issue",
+		Status:      types.StatusOpen,
+		Priority:    1,
+		IssueType:   types.TypeTask,
+	}
+	blocked := &types.Issue{
+		ID:          "test-blocked",
+		Title:       "Blocked",
+		Description: "Is blocked",
+		Status:      types.StatusOpen,
+		Priority:    2,
+		IssueType:   types.TypeTask,
+	}
+	ready := &types.Issue{
+		ID:          "test-ready",
+		Title:       "Ready",
+		Description: "Is ready",
+		Status:      types.StatusOpen,
+		Priority:    3,
+		IssueType:   types.TypeTask,
+	}
+
+	for _, issue := range []*types.Issue{blocker, blocked, ready} {
+		if err := store.CreateIssue(ctx, issue, "tester"); err != nil {
+			t.Fatalf("failed to create issue %s: %v", issue.ID, err)
+		}
+	}
+
+	// Add blocking dependency
+	dep := &types.Dependency{
+		IssueID:     blocked.ID,
+		DependsOnID: blocker.ID,
+		Type:        types.DepBlocks,
+	}
+	if err := store.AddDependency(ctx, dep, "tester"); err != nil {
+		t.Fatalf("failed to add dependency: %v", err)
+	}
+
+	// Get ready work
+	readyWork, err := store.GetReadyWork(ctx, types.WorkFilter{})
+	if err != nil {
+		t.Fatalf("failed to get ready work: %v", err)
+	}
+
+	// Should include blocker and ready, but not blocked
+	foundBlocker := false
+	foundBlocked := false
+	foundReady := false
+	for _, issue := range readyWork {
+		switch issue.ID {
+		case blocker.ID:
+			foundBlocker = true
+		case blocked.ID:
+			foundBlocked = true
+		case ready.ID:
+			foundReady = true
+		}
+	}
+
+	if !foundBlocker {
+		t.Error("expected blocker to be in ready work")
+	}
+	if foundBlocked {
+		t.Error("expected blocked issue to NOT be in ready work")
+	}
+	if !foundReady {
+		t.Error("expected ready issue to be in ready work")
+	}
+}

internal/storage/dolt/events.go

@@ -0,0 +1,160 @@
+package dolt
+
+import (
+	"context"
+	"database/sql"
+	"fmt"
+	"time"
+
+	"github.com/steveyegge/beads/internal/types"
+)
+
+// AddComment adds a comment event to an issue
+func (s *DoltStore) AddComment(ctx context.Context, issueID, actor, comment string) error {
+	_, err := s.db.ExecContext(ctx, `
+		INSERT INTO events (issue_id, event_type, actor, comment)
+		VALUES (?, ?, ?, ?)
+	`, issueID, types.EventCommented, actor, comment)
+	if err != nil {
+		return fmt.Errorf("failed to add comment: %w", err)
+	}
+	return nil
+}
+
+// GetEvents retrieves events for an issue
+func (s *DoltStore) GetEvents(ctx context.Context, issueID string, limit int) ([]*types.Event, error) {
+	query := `
+		SELECT id, issue_id, event_type, actor, old_value, new_value, comment, created_at
+		FROM events
+		WHERE issue_id = ?
+		ORDER BY created_at DESC
+	`
+	args := []interface{}{issueID}
+
+	if limit > 0 {
+		query += fmt.Sprintf(" LIMIT %d", limit)
+	}
+
+	rows, err := s.db.QueryContext(ctx, query, args...)
+	if err != nil {
+		return nil, fmt.Errorf("failed to get events: %w", err)
+	}
+	defer rows.Close()
+
+	var events []*types.Event
+	for rows.Next() {
+		var event types.Event
+		var oldValue, newValue, comment sql.NullString
+		if err := rows.Scan(&event.ID, &event.IssueID, &event.EventType, &event.Actor,
+			&oldValue, &newValue, &comment, &event.CreatedAt); err != nil {
+			return nil, fmt.Errorf("failed to scan event: %w", err)
+		}
+		if oldValue.Valid {
+			event.OldValue = &oldValue.String
+		}
+		if newValue.Valid {
+			event.NewValue = &newValue.String
+		}
+		if comment.Valid {
+			event.Comment = &comment.String
+		}
+		events = append(events, &event)
+	}
+	return events, rows.Err()
+}
+
+// AddIssueComment adds a comment to an issue (structured comment)
+func (s *DoltStore) AddIssueComment(ctx context.Context, issueID, author, text string) (*types.Comment, error) {
+	result, err := s.db.ExecContext(ctx, `
+		INSERT INTO comments (issue_id, author, text, created_at)
+		VALUES (?, ?, ?, ?)
+	`, issueID, author, text, time.Now())
+	if err != nil {
+		return nil, fmt.Errorf("failed to add comment: %w", err)
+	}
+
+	id, err := result.LastInsertId()
+	if err != nil {
+		return nil, fmt.Errorf("failed to get comment id: %w", err)
+	}
+
+	return &types.Comment{
+		ID:        id,
+		IssueID:   issueID,
+		Author:    author,
+		Text:      text,
+		CreatedAt: time.Now(),
+	}, nil
+}
+
+// GetIssueComments retrieves all comments for an issue
+func (s *DoltStore) GetIssueComments(ctx context.Context, issueID string) ([]*types.Comment, error) {
+	rows, err := s.db.QueryContext(ctx, `
+		SELECT id, issue_id, author, text, created_at
+		FROM comments
+		WHERE issue_id = ?
+		ORDER BY created_at ASC
+	`, issueID)
+	if err != nil {
+		return nil, fmt.Errorf("failed to get comments: %w", err)
+	}
+	defer rows.Close()
+
+	var comments []*types.Comment
+	for rows.Next() {
+		var c types.Comment
+		if err := rows.Scan(&c.ID, &c.IssueID, &c.Author, &c.Text, &c.CreatedAt); err != nil {
+			return nil, fmt.Errorf("failed to scan comment: %w", err)
+		}
+		comments = append(comments, &c)
+	}
+	return comments, rows.Err()
+}
+
+// GetCommentsForIssues retrieves comments for multiple issues
+func (s *DoltStore) GetCommentsForIssues(ctx context.Context, issueIDs []string) (map[string][]*types.Comment, error) {
+	if len(issueIDs) == 0 {
+		return make(map[string][]*types.Comment), nil
+	}
+
+	placeholders := make([]string, len(issueIDs))
+	args := make([]interface{}, len(issueIDs))
+	for i, id := range issueIDs {
+		placeholders[i] = "?"
+		args[i] = id
+	}
+
+	query := fmt.Sprintf(`
+		SELECT id, issue_id, author, text, created_at
+		FROM comments
+		WHERE issue_id IN (%s)
+		ORDER BY issue_id, created_at ASC
+	`, joinStrings(placeholders, ","))
+
+	rows, err := s.db.QueryContext(ctx, query, args...)
+	if err != nil {
+		return nil, fmt.Errorf("failed to get comments: %w", err)
+	}
+	defer rows.Close()
+
+	result := make(map[string][]*types.Comment)
+	for rows.Next() {
+		var c types.Comment
+		if err := rows.Scan(&c.ID, &c.IssueID, &c.Author, &c.Text, &c.CreatedAt); err != nil {
+			return nil, fmt.Errorf("failed to scan comment: %w", err)
+		}
+		result[c.IssueID] = append(result[c.IssueID], &c)
+	}
+	return result, rows.Err()
+}
+
+func joinStrings(strs []string, sep string) string {
+	if len(strs) == 0 {
+		return ""
+	}
+	result := strs[0]
+	for _, s := range strs[1:] {
+		result += sep + s
+	}
+	return result
+}

internal/storage/dolt/history.go

@@ -0,0 +1,342 @@
+package dolt
+
+import (
+	"context"
+	"database/sql"
+	"fmt"
+	"regexp"
+	"time"
+
+	"github.com/steveyegge/beads/internal/types"
+)
+
+// validRefPattern matches valid Dolt commit hashes (32 hex chars) or branch names
+var validRefPattern = regexp.MustCompile(`^[a-zA-Z0-9_\-]+$`)
+
+// validTablePattern matches valid table names
+var validTablePattern = regexp.MustCompile(`^[a-zA-Z_][a-zA-Z0-9_]*$`)
+
+// validateRef checks if a ref is safe to use in queries
+func validateRef(ref string) error {
+	if ref == "" {
+		return fmt.Errorf("ref cannot be empty")
+	}
+	if len(ref) > 128 {
+		return fmt.Errorf("ref too long")
+	}
+	if !validRefPattern.MatchString(ref) {
+		return fmt.Errorf("invalid ref format: %s", ref)
+	}
+	return nil
+}
+
+// validateTableName checks if a table name is safe to use in queries
+func validateTableName(table string) error {
+	if table == "" {
+		return fmt.Errorf("table name cannot be empty")
+	}
+	if len(table) > 64 {
+		return fmt.Errorf("table name too long")
+	}
+	if !validTablePattern.MatchString(table) {
+		return fmt.Errorf("invalid table name: %s", table)
+	}
+	return nil
+}
+
+// IssueHistory represents an issue at a specific point in history
+type IssueHistory struct {
+	Issue      *types.Issue
+	CommitHash string
+	Committer  string
+	CommitDate time.Time
+}
+
+// GetIssueHistory returns the complete history of an issue
+func (s *DoltStore) GetIssueHistory(ctx context.Context, issueID string) ([]*IssueHistory, error) {
+	rows, err := s.db.QueryContext(ctx, `
+		SELECT
+			id, title, description, design, acceptance_criteria, notes,
+			status, priority, issue_type, assignee, owner, created_by,
+			estimated_minutes, created_at, updated_at, closed_at, close_reason,
+			pinned, mol_type,
+			commit_hash, committer, commit_date
+		FROM dolt_history_issues
+		WHERE id = ?
+		ORDER BY commit_date DESC
+	`, issueID)
+	if err != nil {
+		return nil, fmt.Errorf("failed to get issue history: %w", err)
+	}
+	defer rows.Close()
+
+	var history []*IssueHistory
+	for rows.Next() {
+		var h IssueHistory
+		var issue types.Issue
+		var closedAt sql.NullTime
+		var assignee, owner, createdBy, closeReason, molType sql.NullString
+		var estimatedMinutes sql.NullInt64
+		var pinned sql.NullInt64
+
+		if err := rows.Scan(
+			&issue.ID, &issue.Title, &issue.Description, &issue.Design, &issue.AcceptanceCriteria, &issue.Notes,
+			&issue.Status, &issue.Priority, &issue.IssueType, &assignee, &owner, &createdBy,
+			&estimatedMinutes, &issue.CreatedAt, &issue.UpdatedAt, &closedAt, &closeReason,
+			&pinned, &molType,
+			&h.CommitHash, &h.Committer, &h.CommitDate,
+		); err != nil {
+			return nil, fmt.Errorf("failed to scan history: %w", err)
+		}
+
+		if closedAt.Valid {
+			issue.ClosedAt = &closedAt.Time
+		}
+		if assignee.Valid {
+			issue.Assignee = assignee.String
+		}
+		if owner.Valid {
+			issue.Owner = owner.String
+		}
+		if createdBy.Valid {
+			issue.CreatedBy = createdBy.String
+		}
+		if estimatedMinutes.Valid {
+			mins := int(estimatedMinutes.Int64)
+			issue.EstimatedMinutes = &mins
+		}
+		if closeReason.Valid {
+			issue.CloseReason = closeReason.String
+		}
+		if pinned.Valid && pinned.Int64 != 0 {
+			issue.Pinned = true
+		}
+		if molType.Valid {
+			issue.MolType = types.MolType(molType.String)
+		}
+
+		h.Issue = &issue
+		history = append(history, &h)
+	}
+
+	return history, rows.Err()
+}
+
+// GetIssueAsOf returns an issue as it existed at a specific commit or time
+func (s *DoltStore) GetIssueAsOf(ctx context.Context, issueID string, ref string) (*types.Issue, error) {
+	// Validate ref to prevent SQL injection
+	if err := validateRef(ref); err != nil {
+		return nil, fmt.Errorf("invalid ref: %w", err)
+	}
+
+	var issue types.Issue
+	var closedAt sql.NullTime
+	var assignee, owner, contentHash sql.NullString
+	var estimatedMinutes sql.NullInt64
+
+	// Note: AS OF requires literal value, but we've validated ref is safe
+	query := fmt.Sprintf(`
+		SELECT id, content_hash, title, description, status, priority, issue_type, assignee, estimated_minutes,
+		       created_at, created_by, owner, updated_at, closed_at
+		FROM issues AS OF '%s'
+		WHERE id = ?
+	`, ref)
+
+	err := s.db.QueryRowContext(ctx, query, issueID).Scan(
+		&issue.ID, &contentHash, &issue.Title, &issue.Description, &issue.Status, &issue.Priority, &issue.IssueType, &assignee, &estimatedMinutes,
+		&issue.CreatedAt, &issue.CreatedBy, &owner, &issue.UpdatedAt, &closedAt,
+	)
+
+	if err == sql.ErrNoRows {
+		return nil, nil
+	}
+	if err != nil {
+		return nil, fmt.Errorf("failed to get issue as of %s: %w", ref, err)
+	}
+
+	if contentHash.Valid {
+		issue.ContentHash = contentHash.String
+	}
+	if closedAt.Valid {
+		issue.ClosedAt = &closedAt.Time
+	}
+	if assignee.Valid {
+		issue.Assignee = assignee.String
+	}
+	if owner.Valid {
+		issue.Owner = owner.String
+	}
+	if estimatedMinutes.Valid {
+		mins := int(estimatedMinutes.Int64)
+		issue.EstimatedMinutes = &mins
+	}
+
+	return &issue, nil
+}
+
+// DiffEntry represents a change between two commits
+type DiffEntry struct {
+	TableName  string
+	DiffType   string // "added", "modified", "removed"
+	FromCommit string
+	ToCommit   string
+	RowID      string
+}
+
+// GetDiff returns changes between two commits
+func (s *DoltStore) GetDiff(ctx context.Context, fromRef, toRef string) ([]*DiffEntry, error) {
+	rows, err := s.db.QueryContext(ctx, `
+		SELECT table_name, diff_type, from_commit, to_commit
+		FROM dolt_diff(?, ?)
+	`, fromRef, toRef)
+	if err != nil {
+		return nil, fmt.Errorf("failed to get diff: %w", err)
+	}
+	defer rows.Close()
+
+	var entries []*DiffEntry
+	for rows.Next() {
+		var e DiffEntry
+		if err := rows.Scan(&e.TableName, &e.DiffType, &e.FromCommit, &e.ToCommit); err != nil {
+			return nil, fmt.Errorf("failed to scan diff entry: %w", err)
+		}
+		entries = append(entries, &e)
+	}
+
+	return entries, rows.Err()
+}
+
+// GetIssueDiff returns detailed changes to a specific issue between commits
+func (s *DoltStore) GetIssueDiff(ctx context.Context, issueID, fromRef, toRef string) (*IssueDiff, error) {
+	// Validate refs to prevent SQL injection
+	if err := validateRef(fromRef); err != nil {
+		return nil, fmt.Errorf("invalid fromRef: %w", err)
+	}
+	if err := validateRef(toRef); err != nil {
+		return nil, fmt.Errorf("invalid toRef: %w", err)
+	}
+
+	// Note: dolt_diff_issues requires literal values, but we've validated refs are safe
+	query := fmt.Sprintf(`
+		SELECT
+			from_id, to_id,
+			from_title, to_title,
+			from_status, to_status,
+			from_description, to_description,
+			diff_type
+		FROM dolt_diff_issues('%s', '%s')
+		WHERE from_id = ? OR to_id = ?
+	`, fromRef, toRef)
+
+	var diff IssueDiff
+	var fromID, toID, fromTitle, toTitle, fromStatus, toStatus sql.NullString
+	var fromDesc, toDesc sql.NullString
+
+	err := s.db.QueryRowContext(ctx, query, issueID, issueID).Scan(
+		&fromID, &toID,
+		&fromTitle, &toTitle,
+		&fromStatus, &toStatus,
+		&fromDesc, &toDesc,
+		&diff.DiffType,
+	)
+
+	if err == sql.ErrNoRows {
+		return nil, nil
+	}
+	if err != nil {
+		return nil, fmt.Errorf("failed to get issue diff: %w", err)
+	}
+
+	if fromID.Valid {
+		diff.FromID = fromID.String
+	}
+	if toID.Valid {
+		diff.ToID = toID.String
+	}
+	if fromTitle.Valid {
+		diff.FromTitle = fromTitle.String
+	}
+	if toTitle.Valid {
+		diff.ToTitle = toTitle.String
+	}
+	if fromStatus.Valid {
+		diff.FromStatus = fromStatus.String
+	}
+	if toStatus.Valid {
+		diff.ToStatus = toStatus.String
+	}
+	if fromDesc.Valid {
+		diff.FromDescription = fromDesc.String
+	}
+	if toDesc.Valid {
+		diff.ToDescription = toDesc.String
+	}
+
+	return &diff, nil
+}
+
+// IssueDiff represents changes to an issue between two commits
+type IssueDiff struct {
+	DiffType        string // "added", "modified", "removed"
+	FromID          string
+	ToID            string
+	FromTitle       string
+	ToTitle         string
+	FromStatus      string
+	ToStatus        string
+	FromDescription string
+	ToDescription   string
+}
+
+// GetConflicts returns any merge conflicts in the current state
+func (s *DoltStore) GetConflicts(ctx context.Context) ([]*Conflict, error) {
+	rows, err := s.db.QueryContext(ctx, `
+		SELECT table_name, num_conflicts FROM dolt_conflicts
+	`)
+	if err != nil {
+		return nil, fmt.Errorf("failed to get conflicts: %w", err)
+	}
+	defer rows.Close()
+
+	var conflicts []*Conflict
+	for rows.Next() {
+		var c Conflict
+		if err := rows.Scan(&c.TableName, &c.NumConflicts); err != nil {
+			return nil, fmt.Errorf("failed to scan conflict: %w", err)
+		}
+		conflicts = append(conflicts, &c)
+	}
+
+	return conflicts, rows.Err()
+}
+
+// Conflict represents a merge conflict
+type Conflict struct {
+	TableName    string
+	NumConflicts int
+}
+
+// ResolveConflicts resolves conflicts using the specified strategy
+func (s *DoltStore) ResolveConflicts(ctx context.Context, table string, strategy string) error {
+	// Validate table name to prevent SQL injection
+	if err := validateTableName(table); err != nil {
+		return fmt.Errorf("invalid table name: %w", err)
+	}
+
+	var query string
+	switch strategy {
+	case "ours":
+		// Note: DOLT_CONFLICTS_RESOLVE requires literal value, but we've validated table is safe
+		query = fmt.Sprintf("CALL DOLT_CONFLICTS_RESOLVE('--ours', '%s')", table)
+	case "theirs":
+		query = fmt.Sprintf("CALL DOLT_CONFLICTS_RESOLVE('--theirs', '%s')", table)
+	default:
+		return fmt.Errorf("unknown conflict resolution strategy: %s", strategy)
+	}
+
+	_, err := s.db.ExecContext(ctx, query)
+	if err != nil {
+		return fmt.Errorf("failed to resolve conflicts: %w", err)
+	}
+	return nil
+}

internal/storage/dolt/issues.go

@@ -0,0 +1,726 @@
+package dolt
+
+import (
+	"context"
+	"database/sql"
+	"encoding/json"
+	"fmt"
+	"strings"
+	"time"
+
+	"github.com/steveyegge/beads/internal/types"
+)
+
+// CreateIssue creates a new issue
+func (s *DoltStore) CreateIssue(ctx context.Context, issue *types.Issue, actor string) error {
+	// Fetch custom statuses and types for validation
+	customStatuses, err := s.GetCustomStatuses(ctx)
+	if err != nil {
+		return fmt.Errorf("failed to get custom statuses: %w", err)
+	}
+	customTypes, err := s.GetCustomTypes(ctx)
+	if err != nil {
+		return fmt.Errorf("failed to get custom types: %w", err)
+	}
+
+	// Set timestamps
+	now := time.Now()
+	if issue.CreatedAt.IsZero() {
+		issue.CreatedAt = now
+	}
+	if issue.UpdatedAt.IsZero() {
+		issue.UpdatedAt = now
+	}
+
+	// Defensive fix for closed_at invariant
+	if issue.Status == types.StatusClosed && issue.ClosedAt == nil {
+		maxTime := issue.CreatedAt
+		if issue.UpdatedAt.After(maxTime) {
+			maxTime = issue.UpdatedAt
+		}
+		closedAt := maxTime.Add(time.Second)
+		issue.ClosedAt = &closedAt
+	}
+
+	// Defensive fix for deleted_at invariant
+	if issue.Status == types.StatusTombstone && issue.DeletedAt == nil {
+		maxTime := issue.CreatedAt
+		if issue.UpdatedAt.After(maxTime) {
+			maxTime = issue.UpdatedAt
+		}
+		deletedAt := maxTime.Add(time.Second)
+		issue.DeletedAt = &deletedAt
+	}
+
+	// Validate issue
+	if err := issue.ValidateWithCustom(customStatuses, customTypes); err != nil {
+		return fmt.Errorf("validation failed: %w", err)
+	}
+
+	// Compute content hash
+	if issue.ContentHash == "" {
+		issue.ContentHash = issue.ComputeContentHash()
+	}
+
+	// Start transaction
+	tx, err := s.db.BeginTx(ctx, nil)
+	if err != nil {
+		return fmt.Errorf("failed to begin transaction: %w", err)
+	}
+	defer func() { _ = tx.Rollback() }()
+
+	// Get prefix from config
+	var configPrefix string
+	err = tx.QueryRowContext(ctx, "SELECT value FROM config WHERE `key` = ?", "issue_prefix").Scan(&configPrefix)
+	if err == sql.ErrNoRows || configPrefix == "" {
+		return fmt.Errorf("database not initialized: issue_prefix config is missing (run 'bd init --prefix <prefix>' first)")
+	} else if err != nil {
+		return fmt.Errorf("failed to get config: %w", err)
+	}
+
+	// Determine prefix for ID generation
+	prefix := configPrefix
+	if issue.PrefixOverride != "" {
+		prefix = issue.PrefixOverride
+	} else if issue.IDPrefix != "" {
+		prefix = configPrefix + "-" + issue.IDPrefix
+	}
+
+	// Generate or validate ID
+	if issue.ID == "" {
+		generatedID, err := generateIssueID(ctx, tx, prefix, issue, actor)
+		if err != nil {
+			return fmt.Errorf("failed to generate issue ID: %w", err)
+		}
+		issue.ID = generatedID
+	}
+
+	// Insert issue
+	if err := insertIssue(ctx, tx, issue); err != nil {
+		return fmt.Errorf("failed to insert issue: %w", err)
+	}
+
+	// Record creation event
+	if err := recordEvent(ctx, tx, issue.ID, types.EventCreated, actor, "", ""); err != nil {
+		return fmt.Errorf("failed to record creation event: %w", err)
+	}
+
+	// Mark issue as dirty
+	if err := markDirty(ctx, tx, issue.ID); err != nil {
+		return fmt.Errorf("failed to mark issue dirty: %w", err)
+	}
+
+	return tx.Commit()
+}
+
+// CreateIssues creates multiple issues in a single transaction
+func (s *DoltStore) CreateIssues(ctx context.Context, issues []*types.Issue, actor string) error {
+	if len(issues) == 0 {
+		return nil
+	}
+
+	// Fetch custom statuses and types for validation
+	customStatuses, err := s.GetCustomStatuses(ctx)
+	if err != nil {
+		return fmt.Errorf("failed to get custom statuses: %w", err)
+	}
+	customTypes, err := s.GetCustomTypes(ctx)
+	if err != nil {
+		return fmt.Errorf("failed to get custom types: %w", err)
+	}
+
+	tx, err := s.db.BeginTx(ctx, nil)
+	if err != nil {
+		return fmt.Errorf("failed to begin transaction: %w", err)
+	}
+	defer func() { _ = tx.Rollback() }()
+
+	for _, issue := range issues {
+		now := time.Now()
+		if issue.CreatedAt.IsZero() {
+			issue.CreatedAt = now
+		}
+		if issue.UpdatedAt.IsZero() {
+			issue.UpdatedAt = now
+		}
+
+		// Defensive fix for closed_at invariant
+		if issue.Status == types.StatusClosed && issue.ClosedAt == nil {
+			maxTime := issue.CreatedAt
+			if issue.UpdatedAt.After(maxTime) {
+				maxTime = issue.UpdatedAt
+			}
+			closedAt := maxTime.Add(time.Second)
+			issue.ClosedAt = &closedAt
+		}
+
+		// Defensive fix for deleted_at invariant
+		if issue.Status == types.StatusTombstone && issue.DeletedAt == nil {
+			maxTime := issue.CreatedAt
+			if issue.UpdatedAt.After(maxTime) {
+				maxTime = issue.UpdatedAt
+			}
+			deletedAt := maxTime.Add(time.Second)
+			issue.DeletedAt = &deletedAt
+		}
+
+		// Validate issue
+		if err := issue.ValidateWithCustom(customStatuses, customTypes); err != nil {
+			return fmt.Errorf("validation failed for issue %s: %w", issue.ID, err)
+		}
+
+		if issue.ContentHash == "" {
+			issue.ContentHash = issue.ComputeContentHash()
+		}
+
+		if err := insertIssue(ctx, tx, issue); err != nil {
+			return fmt.Errorf("failed to insert issue %s: %w", issue.ID, err)
+		}
+		if err := recordEvent(ctx, tx, issue.ID, types.EventCreated, actor, "", ""); err != nil {
+			return fmt.Errorf("failed to record event for %s: %w", issue.ID, err)
+		}
+		if err := markDirty(ctx, tx, issue.ID); err != nil {
+			return fmt.Errorf("failed to mark dirty %s: %w", issue.ID, err)
+		}
+	}
+
+	return tx.Commit()
+}
+
+// GetIssue retrieves an issue by ID
+func (s *DoltStore) GetIssue(ctx context.Context, id string) (*types.Issue, error) {
+	s.mu.RLock()
+	defer s.mu.RUnlock()
+
+	issue, err := scanIssue(ctx, s.db, id)
+	if err != nil {
+		return nil, err
+	}
+	if issue == nil {
+		return nil, nil
+	}
+
+	// Fetch labels
+	labels, err := s.GetLabels(ctx, issue.ID)
+	if err != nil {
+		return nil, fmt.Errorf("failed to get labels: %w", err)
+	}
+	issue.Labels = labels
+
+	return issue, nil
+}
+
+// GetIssueByExternalRef retrieves an issue by external reference
+func (s *DoltStore) GetIssueByExternalRef(ctx context.Context, externalRef string) (*types.Issue, error) {
+	s.mu.RLock()
+	defer s.mu.RUnlock()
+
+	var id string
+	err := s.db.QueryRowContext(ctx, "SELECT id FROM issues WHERE external_ref = ?", externalRef).Scan(&id)
+	if err == sql.ErrNoRows {
+		return nil, nil
+	}
+	if err != nil {
+		return nil, fmt.Errorf("failed to get issue by external_ref: %w", err)
+	}
+
+	return s.GetIssue(ctx, id)
+}
+
+// UpdateIssue updates fields on an issue
+func (s *DoltStore) UpdateIssue(ctx context.Context, id string, updates map[string]interface{}, actor string) error {
+	oldIssue, err := s.GetIssue(ctx, id)
+	if err != nil {
+		return fmt.Errorf("failed to get issue for update: %w", err)
+	}
+	if oldIssue == nil {
+		return fmt.Errorf("issue %s not found", id)
+	}
+
+	// Build update query
+	setClauses := []string{"updated_at = ?"}
+	args := []interface{}{time.Now()}
+
+	for key, value := range updates {
+		if !isAllowedUpdateField(key) {
+			return fmt.Errorf("invalid field for update: %s", key)
+		}
+
+		columnName := key
+		if key == "wisp" {
+			columnName = "ephemeral"
+		}
+		setClauses = append(setClauses, fmt.Sprintf("`%s` = ?", columnName))
+		args = append(args, value)
+	}
+
+	// Auto-manage closed_at
+	setClauses, args = manageClosedAt(oldIssue, updates, setClauses, args)
+
+	args = append(args, id)
+
+	tx, err := s.db.BeginTx(ctx, nil)
+	if err != nil {
+		return fmt.Errorf("failed to begin transaction: %w", err)
+	}
+	defer func() { _ = tx.Rollback() }()
+
+	query := fmt.Sprintf("UPDATE issues SET %s WHERE id = ?", strings.Join(setClauses, ", "))
+	if _, err := tx.ExecContext(ctx, query, args...); err != nil {
+		return fmt.Errorf("failed to update issue: %w", err)
+	}
+
+	// Record event
+	oldData, _ := json.Marshal(oldIssue)
+	newData, _ := json.Marshal(updates)
+	eventType := determineEventType(oldIssue, updates)
+
+	if err := recordEvent(ctx, tx, id, eventType, actor, string(oldData), string(newData)); err != nil {
+		return fmt.Errorf("failed to record event: %w", err)
+	}
+
+	if err := markDirty(ctx, tx, id); err != nil {
+		return fmt.Errorf("failed to mark dirty: %w", err)
+	}
+
+	return tx.Commit()
+}
+
+// CloseIssue closes an issue with a reason
+func (s *DoltStore) CloseIssue(ctx context.Context, id string, reason string, actor string, session string) error {
+	now := time.Now()
+
+	tx, err := s.db.BeginTx(ctx, nil)
+	if err != nil {
+		return fmt.Errorf("failed to begin transaction: %w", err)
+	}
+	defer func() { _ = tx.Rollback() }()
+
+	result, err := tx.ExecContext(ctx, `
+		UPDATE issues SET status = ?, closed_at = ?, updated_at = ?, close_reason = ?, closed_by_session = ?
+		WHERE id = ?
+	`, types.StatusClosed, now, now, reason, session, id)
+	if err != nil {
+		return fmt.Errorf("failed to close issue: %w", err)
+	}
+
+	rows, err := result.RowsAffected()
+	if err != nil {
+		return fmt.Errorf("failed to get rows affected: %w", err)
+	}
+	if rows == 0 {
+		return fmt.Errorf("issue not found: %s", id)
+	}
+
+	if err := recordEvent(ctx, tx, id, types.EventClosed, actor, "", reason); err != nil {
+		return fmt.Errorf("failed to record event: %w", err)
+	}
+
+	if err := markDirty(ctx, tx, id); err != nil {
+		return fmt.Errorf("failed to mark dirty: %w", err)
+	}
+
+	return tx.Commit()
+}
+
+// DeleteIssue permanently removes an issue
+func (s *DoltStore) DeleteIssue(ctx context.Context, id string) error {
+	tx, err := s.db.BeginTx(ctx, nil)
+	if err != nil {
+		return fmt.Errorf("failed to begin transaction: %w", err)
+	}
+	defer func() { _ = tx.Rollback() }()
+
+	// Delete related data (foreign keys will cascade, but be explicit)
+	tables := []string{"dependencies", "events", "comments", "labels", "dirty_issues"}
+	for _, table := range tables {
+		if table == "dependencies" {
+			_, err = tx.ExecContext(ctx, fmt.Sprintf("DELETE FROM %s WHERE issue_id = ? OR depends_on_id = ?", table), id, id)
+		} else {
+			_, err = tx.ExecContext(ctx, fmt.Sprintf("DELETE FROM %s WHERE issue_id = ?", table), id)
+		}
+		if err != nil {
+			return fmt.Errorf("failed to delete from %s: %w", table, err)
+		}
+	}
+
+	result, err := tx.ExecContext(ctx, "DELETE FROM issues WHERE id = ?", id)
+	if err != nil {
+		return fmt.Errorf("failed to delete issue: %w", err)
+	}
+
+	rows, err := result.RowsAffected()
+	if err != nil {
+		return fmt.Errorf("failed to get rows affected: %w", err)
+	}
+	if rows == 0 {
+		return fmt.Errorf("issue not found: %s", id)
+	}
+
+	return tx.Commit()
+}
+
+// =============================================================================
+// Helper functions
+// =============================================================================
+
+func insertIssue(ctx context.Context, tx *sql.Tx, issue *types.Issue) error {
+	_, err := tx.ExecContext(ctx, `
+		INSERT INTO issues (
+			id, content_hash, title, description, design, acceptance_criteria, notes,
+			status, priority, issue_type, assignee, estimated_minutes,
+			created_at, created_by, owner, updated_at, closed_at, external_ref,
+			compaction_level, compacted_at, compacted_at_commit, original_size,
+			deleted_at, deleted_by, delete_reason, original_type,
+			sender, ephemeral, pinned, is_template, crystallizes,
+			mol_type, work_type, quality_score, source_system, source_repo, close_reason,
+			event_kind, actor, target, payload,
+			await_type, await_id, timeout_ns, waiters,
+			hook_bead, role_bead, agent_state, last_activity, role_type, rig,
+			due_at, defer_until
+		) VALUES (
+			?, ?, ?, ?, ?, ?, ?,
+			?, ?, ?, ?, ?,
+			?, ?, ?, ?, ?, ?,
+			?, ?, ?, ?,
+			?, ?, ?, ?,
+			?, ?, ?, ?, ?,
+			?, ?, ?, ?, ?, ?,
+			?, ?, ?, ?,
+			?, ?, ?, ?,
+			?, ?, ?, ?, ?, ?,
+			?, ?
+		)
+	`,
+		issue.ID, issue.ContentHash, issue.Title, issue.Description, issue.Design, issue.AcceptanceCriteria, issue.Notes,
+		issue.Status, issue.Priority, issue.IssueType, nullString(issue.Assignee), nullInt(issue.EstimatedMinutes),
+		issue.CreatedAt, issue.CreatedBy, issue.Owner, issue.UpdatedAt, issue.ClosedAt, nullStringPtr(issue.ExternalRef),
+		issue.CompactionLevel, issue.CompactedAt, nullStringPtr(issue.CompactedAtCommit), nullIntVal(issue.OriginalSize),
+		issue.DeletedAt, issue.DeletedBy, issue.DeleteReason, issue.OriginalType,
+		issue.Sender, issue.Ephemeral, issue.Pinned, issue.IsTemplate, issue.Crystallizes,
+		issue.MolType, issue.WorkType, issue.QualityScore, issue.SourceSystem, issue.SourceRepo, issue.CloseReason,
+		issue.EventKind, issue.Actor, issue.Target, issue.Payload,
+		issue.AwaitType, issue.AwaitID, issue.Timeout.Nanoseconds(), formatJSONStringArray(issue.Waiters),
+		issue.HookBead, issue.RoleBead, issue.AgentState, issue.LastActivity, issue.RoleType, issue.Rig,
+		issue.DueAt, issue.DeferUntil,
+	)
+	return err
+}
+
+func scanIssue(ctx context.Context, db *sql.DB, id string) (*types.Issue, error) {
+	var issue types.Issue
+	var closedAt, compactedAt, deletedAt, lastActivity, dueAt, deferUntil sql.NullTime
+	var estimatedMinutes, originalSize, timeoutNs sql.NullInt64
+	var assignee, externalRef, compactedAtCommit, owner sql.NullString
+	var contentHash, sourceRepo, closeReason, deletedBy, deleteReason, originalType sql.NullString
+	var workType, sourceSystem sql.NullString
+	var sender, molType, eventKind, actor, target, payload sql.NullString
+	var awaitType, awaitID, waiters sql.NullString
+	var hookBead, roleBead, agentState, roleType, rig sql.NullString
+	var ephemeral, pinned, isTemplate, crystallizes sql.NullInt64
+	var qualityScore sql.NullFloat64
+
+	err := db.QueryRowContext(ctx, `
+		SELECT id, content_hash, title, description, design, acceptance_criteria, notes,
+		       status, priority, issue_type, assignee, estimated_minutes,
+		       created_at, created_by, owner, updated_at, closed_at, external_ref,
+		       compaction_level, compacted_at, compacted_at_commit, original_size, source_repo, close_reason,
+		       deleted_at, deleted_by, delete_reason, original_type,
+		       sender, ephemeral, pinned, is_template, crystallizes,
+		       await_type, await_id, timeout_ns, waiters,
+		       hook_bead, role_bead, agent_state, last_activity, role_type, rig, mol_type,
+		       event_kind, actor, target, payload,
+		       due_at, defer_until,
+		       quality_score, work_type, source_system
+		FROM issues
+		WHERE id = ?
+	`, id).Scan(
+		&issue.ID, &contentHash, &issue.Title, &issue.Description, &issue.Design,
+		&issue.AcceptanceCriteria, &issue.Notes, &issue.Status,
+		&issue.Priority, &issue.IssueType, &assignee, &estimatedMinutes,
+		&issue.CreatedAt, &issue.CreatedBy, &owner, &issue.UpdatedAt, &closedAt, &externalRef,
+		&issue.CompactionLevel, &compactedAt, &compactedAtCommit, &originalSize, &sourceRepo, &closeReason,
+		&deletedAt, &deletedBy, &deleteReason, &originalType,
+		&sender, &ephemeral, &pinned, &isTemplate, &crystallizes,
+		&awaitType, &awaitID, &timeoutNs, &waiters,
+		&hookBead, &roleBead, &agentState, &lastActivity, &roleType, &rig, &molType,
+		&eventKind, &actor, &target, &payload,
+		&dueAt, &deferUntil,
+		&qualityScore, &workType, &sourceSystem,
+	)
+
+	if err == sql.ErrNoRows {
+		return nil, nil
+	}
+	if err != nil {
+		return nil, fmt.Errorf("failed to get issue: %w", err)
+	}
+
+	// Map nullable fields
+	if contentHash.Valid {
+		issue.ContentHash = contentHash.String
+	}
+	if closedAt.Valid {
+		issue.ClosedAt = &closedAt.Time
+	}
+	if estimatedMinutes.Valid {
+		mins := int(estimatedMinutes.Int64)
+		issue.EstimatedMinutes = &mins
+	}
+	if assignee.Valid {
+		issue.Assignee = assignee.String
+	}
+	if owner.Valid {
+		issue.Owner = owner.String
+	}
+	if externalRef.Valid {
+		issue.ExternalRef = &externalRef.String
+	}
+	if compactedAt.Valid {
+		issue.CompactedAt = &compactedAt.Time
+	}
+	if compactedAtCommit.Valid {
+		issue.CompactedAtCommit = &compactedAtCommit.String
+	}
+	if originalSize.Valid {
+		issue.OriginalSize = int(originalSize.Int64)
+	}
+	if sourceRepo.Valid {
+		issue.SourceRepo = sourceRepo.String
+	}
+	if closeReason.Valid {
+		issue.CloseReason = closeReason.String
+	}
+	if deletedAt.Valid {
+		issue.DeletedAt = &deletedAt.Time
+	}
+	if deletedBy.Valid {
+		issue.DeletedBy = deletedBy.String
+	}
+	if deleteReason.Valid {
+		issue.DeleteReason = deleteReason.String
+	}
+	if originalType.Valid {
+		issue.OriginalType = originalType.String
+	}
+	if sender.Valid {
+		issue.Sender = sender.String
+	}
+	if ephemeral.Valid && ephemeral.Int64 != 0 {
+		issue.Ephemeral = true
+	}
+	if pinned.Valid && pinned.Int64 != 0 {
+		issue.Pinned = true
+	}
+	if isTemplate.Valid && isTemplate.Int64 != 0 {
+		issue.IsTemplate = true
+	}
+	if crystallizes.Valid && crystallizes.Int64 != 0 {
+		issue.Crystallizes = true
+	}
+	if awaitType.Valid {
+		issue.AwaitType = awaitType.String
+	}
+	if awaitID.Valid {
+		issue.AwaitID = awaitID.String
+	}
+	if timeoutNs.Valid {
+		issue.Timeout = time.Duration(timeoutNs.Int64)
+	}
+	if waiters.Valid && waiters.String != "" {
+		issue.Waiters = parseJSONStringArray(waiters.String)
+	}
+	if hookBead.Valid {
+		issue.HookBead = hookBead.String
+	}
+	if roleBead.Valid {
+		issue.RoleBead = roleBead.String
+	}
+	if agentState.Valid {
+		issue.AgentState = types.AgentState(agentState.String)
+	}
+	if lastActivity.Valid {
+		issue.LastActivity = &lastActivity.Time
+	}
+	if roleType.Valid {
+		issue.RoleType = roleType.String
+	}
+	if rig.Valid {
+		issue.Rig = rig.String
+	}
+	if molType.Valid {
+		issue.MolType = types.MolType(molType.String)
+	}
+	if eventKind.Valid {
+		issue.EventKind = eventKind.String
+	}
+	if actor.Valid {
+		issue.Actor = actor.String
+	}
+	if target.Valid {
+		issue.Target = target.String
+	}
+	if payload.Valid {
+		issue.Payload = payload.String
+	}
+	if dueAt.Valid {
+		issue.DueAt = &dueAt.Time
+	}
+	if deferUntil.Valid {
+		issue.DeferUntil = &deferUntil.Time
+	}
+	if qualityScore.Valid {
+		qs := float32(qualityScore.Float64)
+		issue.QualityScore = &qs
+	}
+	if workType.Valid {
+		issue.WorkType = types.WorkType(workType.String)
+	}
+	if sourceSystem.Valid {
+		issue.SourceSystem = sourceSystem.String
+	}
+
+	return &issue, nil
+}
+
+func recordEvent(ctx context.Context, tx *sql.Tx, issueID string, eventType types.EventType, actor, oldValue, newValue string) error {
+	_, err := tx.ExecContext(ctx, `
+		INSERT INTO events (issue_id, event_type, actor, old_value, new_value)
+		VALUES (?, ?, ?, ?, ?)
+	`, issueID, eventType, actor, oldValue, newValue)
+	return err
+}
+
+func markDirty(ctx context.Context, tx *sql.Tx, issueID string) error {
+	_, err := tx.ExecContext(ctx, `
+		INSERT INTO dirty_issues (issue_id, marked_at)
+		VALUES (?, ?)
+		ON DUPLICATE KEY UPDATE marked_at = VALUES(marked_at)
+	`, issueID, time.Now())
+	return err
+}
+
+func generateIssueID(ctx context.Context, tx *sql.Tx, prefix string, issue *types.Issue, actor string) (string, error) {
+	// Simple hash-based ID generation
+	// Use first 6 chars of content hash
+	hash := issue.ComputeContentHash()
+	if len(hash) > 6 {
+		hash = hash[:6]
+	}
+	return fmt.Sprintf("%s-%s", prefix, hash), nil
+}
+
+func isAllowedUpdateField(key string) bool {
+	allowed := map[string]bool{
+		"status": true, "priority": true, "title": true, "assignee": true,
+		"description": true, "design": true, "acceptance_criteria": true, "notes": true,
+		"issue_type": true, "estimated_minutes": true, "external_ref": true,
+		"closed_at": true, "close_reason": true, "closed_by_session": true,
+		"sender": true, "wisp": true, "pinned": true,
+		"hook_bead": true, "role_bead": true, "agent_state": true, "last_activity": true,
+		"role_type": true, "rig": true, "mol_type": true,
+		"event_category": true, "event_actor": true, "event_target": true, "event_payload": true,
+		"due_at": true, "defer_until": true, "await_id": true,
+	}
+	return allowed[key]
+}
+
+func manageClosedAt(oldIssue *types.Issue, updates map[string]interface{}, setClauses []string, args []interface{}) ([]string, []interface{}) {
+	statusVal, hasStatus := updates["status"]
+	_, hasExplicitClosedAt := updates["closed_at"]
+	if hasExplicitClosedAt || !hasStatus {
+		return setClauses, args
+	}
+
+	var newStatus string
+	switch v := statusVal.(type) {
+	case string:
+		newStatus = v
+	case types.Status:
+		newStatus = string(v)
+	default:
+		return setClauses, args
+	}
+
+	if newStatus == string(types.StatusClosed) {
+		now := time.Now()
+		setClauses = append(setClauses, "closed_at = ?")
+		args = append(args, now)
+	} else if oldIssue.Status == types.StatusClosed {
+		setClauses = append(setClauses, "closed_at = ?", "close_reason = ?")
+		args = append(args, nil, "")
+	}
+
+	return setClauses, args
+}
+
+func determineEventType(oldIssue *types.Issue, updates map[string]interface{}) types.EventType {
+	statusVal, hasStatus := updates["status"]
+	if !hasStatus {
+		return types.EventUpdated
+	}
+
+	newStatus, ok := statusVal.(string)
+	if !ok {
+		return types.EventUpdated
+	}
+
+	if newStatus == string(types.StatusClosed) {
+		return types.EventClosed
+	}
+	if oldIssue.Status == types.StatusClosed {
+		return types.EventReopened
+	}
+	return types.EventStatusChanged
+}
+
+// Helper functions for nullable values
+func nullString(s string) interface{} {
+	if s == "" {
+		return nil
+	}
+	return s
+}
+
+func nullStringPtr(s *string) interface{} {
+	if s == nil {
+		return nil
+	}
+	return *s
+}
+
+func nullInt(i *int) interface{} {
+	if i == nil {
+		return nil
+	}
+	return *i
+}
+
+func nullIntVal(i int) interface{} {
+	if i == 0 {
+		return nil
+	}
+	return i
+}
+
+func parseJSONStringArray(s string) []string {
+	if s == "" {
+		return nil
+	}
+	var result []string
+	if err := json.Unmarshal([]byte(s), &result); err != nil {
+		return nil
+	}
+	return result
+}
+
+func formatJSONStringArray(arr []string) string {
+	if len(arr) == 0 {
+		return ""
+	}
+	data, err := json.Marshal(arr)
+	if err != nil {
+		return ""
+	}
+	return string(data)
+}

internal/storage/dolt/labels.go

@@ -0,0 +1,118 @@
+package dolt
+
+import (
+	"context"
+	"fmt"
+	"strings"
+
+	"github.com/steveyegge/beads/internal/types"
+)
+
+// AddLabel adds a label to an issue
+func (s *DoltStore) AddLabel(ctx context.Context, issueID, label, actor string) error {
+	_, err := s.db.ExecContext(ctx, `
+		INSERT IGNORE INTO labels (issue_id, label) VALUES (?, ?)
+	`, issueID, label)
+	if err != nil {
+		return fmt.Errorf("failed to add label: %w", err)
+	}
+	return nil
+}
+
+// RemoveLabel removes a label from an issue
+func (s *DoltStore) RemoveLabel(ctx context.Context, issueID, label, actor string) error {
+	_, err := s.db.ExecContext(ctx, `
+		DELETE FROM labels WHERE issue_id = ? AND label = ?
+	`, issueID, label)
+	if err != nil {
+		return fmt.Errorf("failed to remove label: %w", err)
+	}
+	return nil
+}
+
+// GetLabels retrieves all labels for an issue
+func (s *DoltStore) GetLabels(ctx context.Context, issueID string) ([]string, error) {
+	rows, err := s.db.QueryContext(ctx, `
+		SELECT label FROM labels WHERE issue_id = ? ORDER BY label
+	`, issueID)
+	if err != nil {
+		return nil, fmt.Errorf("failed to get labels: %w", err)
+	}
+	defer rows.Close()
+
+	var labels []string
+	for rows.Next() {
+		var label string
+		if err := rows.Scan(&label); err != nil {
+			return nil, fmt.Errorf("failed to scan label: %w", err)
+		}
+		labels = append(labels, label)
+	}
+	return labels, rows.Err()
+}
+
+// GetLabelsForIssues retrieves labels for multiple issues
+func (s *DoltStore) GetLabelsForIssues(ctx context.Context, issueIDs []string) (map[string][]string, error) {
+	if len(issueIDs) == 0 {
+		return make(map[string][]string), nil
+	}
+
+	placeholders := make([]string, len(issueIDs))
+	args := make([]interface{}, len(issueIDs))
+	for i, id := range issueIDs {
+		placeholders[i] = "?"
+		args[i] = id
+	}
+
+	query := fmt.Sprintf(`
+		SELECT issue_id, label FROM labels
+		WHERE issue_id IN (%s)
+		ORDER BY issue_id, label
+	`, strings.Join(placeholders, ","))
+
+	rows, err := s.db.QueryContext(ctx, query, args...)
+	if err != nil {
+		return nil, fmt.Errorf("failed to get labels for issues: %w", err)
+	}
+	defer rows.Close()
+
+	result := make(map[string][]string)
+	for rows.Next() {
+		var issueID, label string
+		if err := rows.Scan(&issueID, &label); err != nil {
+			return nil, fmt.Errorf("failed to scan label: %w", err)
+		}
+		result[issueID] = append(result[issueID], label)
+	}
+	return result, rows.Err()
+}
+
+// GetIssuesByLabel retrieves all issues with a specific label
+func (s *DoltStore) GetIssuesByLabel(ctx context.Context, label string) ([]*types.Issue, error) {
+	rows, err := s.db.QueryContext(ctx, `
+		SELECT i.id FROM issues i
+		JOIN labels l ON i.id = l.issue_id
+		WHERE l.label = ?
+		ORDER BY i.priority ASC, i.created_at DESC
+	`, label)
+	if err != nil {
+		return nil, fmt.Errorf("failed to get issues by label: %w", err)
+	}
+	defer rows.Close()
+
+	var issues []*types.Issue
+	for rows.Next() {
+		var id string
+		if err := rows.Scan(&id); err != nil {
+			return nil, fmt.Errorf("failed to scan issue id: %w", err)
+		}
+		issue, err := s.GetIssue(ctx, id)
+		if err != nil {
+			return nil, err
+		}
+		if issue != nil {
+			issues = append(issues, issue)
+		}
+	}
+	return issues, rows.Err()
+}

internal/storage/dolt/queries.go

@@ -0,0 +1,547 @@
+package dolt
+
+import (
+	"context"
+	"database/sql"
+	"fmt"
+	"strings"
+	"time"
+
+	"github.com/steveyegge/beads/internal/types"
+)
+
+// SearchIssues finds issues matching query and filters
+func (s *DoltStore) SearchIssues(ctx context.Context, query string, filter types.IssueFilter) ([]*types.Issue, error) {
+	s.mu.RLock()
+	defer s.mu.RUnlock()
+
+	whereClauses := []string{}
+	args := []interface{}{}
+
+	if query != "" {
+		whereClauses = append(whereClauses, "(title LIKE ? OR description LIKE ? OR id LIKE ?)")
+		pattern := "%" + query + "%"
+		args = append(args, pattern, pattern, pattern)
+	}
+
+	if filter.TitleSearch != "" {
+		whereClauses = append(whereClauses, "title LIKE ?")
+		args = append(args, "%"+filter.TitleSearch+"%")
+	}
+
+	if filter.TitleContains != "" {
+		whereClauses = append(whereClauses, "title LIKE ?")
+		args = append(args, "%"+filter.TitleContains+"%")
+	}
+	if filter.DescriptionContains != "" {
+		whereClauses = append(whereClauses, "description LIKE ?")
+		args = append(args, "%"+filter.DescriptionContains+"%")
+	}
+	if filter.NotesContains != "" {
+		whereClauses = append(whereClauses, "notes LIKE ?")
+		args = append(args, "%"+filter.NotesContains+"%")
+	}
+
+	if filter.Status != nil {
+		whereClauses = append(whereClauses, "status = ?")
+		args = append(args, *filter.Status)
+	} else if !filter.IncludeTombstones {
+		whereClauses = append(whereClauses, "status != ?")
+		args = append(args, types.StatusTombstone)
+	}
+
+	if len(filter.ExcludeStatus) > 0 {
+		placeholders := make([]string, len(filter.ExcludeStatus))
+		for i, s := range filter.ExcludeStatus {
+			placeholders[i] = "?"
+			args = append(args, string(s))
+		}
+		whereClauses = append(whereClauses, fmt.Sprintf("status NOT IN (%s)", strings.Join(placeholders, ",")))
+	}
+
+	if len(filter.ExcludeTypes) > 0 {
+		placeholders := make([]string, len(filter.ExcludeTypes))
+		for i, t := range filter.ExcludeTypes {
+			placeholders[i] = "?"
+			args = append(args, string(t))
+		}
+		whereClauses = append(whereClauses, fmt.Sprintf("issue_type NOT IN (%s)", strings.Join(placeholders, ",")))
+	}
+
+	if filter.Priority != nil {
+		whereClauses = append(whereClauses, "priority = ?")
+		args = append(args, *filter.Priority)
+	}
+	if filter.PriorityMin != nil {
+		whereClauses = append(whereClauses, "priority >= ?")
+		args = append(args, *filter.PriorityMin)
+	}
+	if filter.PriorityMax != nil {
+		whereClauses = append(whereClauses, "priority <= ?")
+		args = append(args, *filter.PriorityMax)
+	}
+
+	if filter.IssueType != nil {
+		whereClauses = append(whereClauses, "issue_type = ?")
+		args = append(args, *filter.IssueType)
+	}
+
+	if filter.Assignee != nil {
+		whereClauses = append(whereClauses, "assignee = ?")
+		args = append(args, *filter.Assignee)
+	}
+
+	// Date ranges
+	if filter.CreatedAfter != nil {
+		whereClauses = append(whereClauses, "created_at > ?")
+		args = append(args, filter.CreatedAfter.Format(time.RFC3339))
+	}
+	if filter.CreatedBefore != nil {
+		whereClauses = append(whereClauses, "created_at < ?")
+		args = append(args, filter.CreatedBefore.Format(time.RFC3339))
+	}
+	if filter.UpdatedAfter != nil {
+		whereClauses = append(whereClauses, "updated_at > ?")
+		args = append(args, filter.UpdatedAfter.Format(time.RFC3339))
+	}
+	if filter.UpdatedBefore != nil {
+		whereClauses = append(whereClauses, "updated_at < ?")
+		args = append(args, filter.UpdatedBefore.Format(time.RFC3339))
+	}
+
+	// Empty/null checks
+	if filter.EmptyDescription {
+		whereClauses = append(whereClauses, "(description IS NULL OR description = '')")
+	}
+	if filter.NoAssignee {
+		whereClauses = append(whereClauses, "(assignee IS NULL OR assignee = '')")
+	}
+	if filter.NoLabels {
+		whereClauses = append(whereClauses, "id NOT IN (SELECT DISTINCT issue_id FROM labels)")
+	}
+
+	// Label filtering (AND)
+	if len(filter.Labels) > 0 {
+		for _, label := range filter.Labels {
+			whereClauses = append(whereClauses, "id IN (SELECT issue_id FROM labels WHERE label = ?)")
+			args = append(args, label)
+		}
+	}
+
+	// Label filtering (OR)
+	if len(filter.LabelsAny) > 0 {
+		placeholders := make([]string, len(filter.LabelsAny))
+		for i, label := range filter.LabelsAny {
+			placeholders[i] = "?"
+			args = append(args, label)
+		}
+		whereClauses = append(whereClauses, fmt.Sprintf("id IN (SELECT issue_id FROM labels WHERE label IN (%s))", strings.Join(placeholders, ", ")))
+	}
+
+	// ID filtering
+	if len(filter.IDs) > 0 {
+		placeholders := make([]string, len(filter.IDs))
+		for i, id := range filter.IDs {
+			placeholders[i] = "?"
+			args = append(args, id)
+		}
+		whereClauses = append(whereClauses, fmt.Sprintf("id IN (%s)", strings.Join(placeholders, ", ")))
+	}
+
+	if filter.IDPrefix != "" {
+		whereClauses = append(whereClauses, "id LIKE ?")
+		args = append(args, filter.IDPrefix+"%")
+	}
+
+	// Wisp filtering
+	if filter.Ephemeral != nil {
+		if *filter.Ephemeral {
+			whereClauses = append(whereClauses, "ephemeral = 1")
+		} else {
+			whereClauses = append(whereClauses, "(ephemeral = 0 OR ephemeral IS NULL)")
+		}
+	}
+
+	// Pinned filtering
+	if filter.Pinned != nil {
+		if *filter.Pinned {
+			whereClauses = append(whereClauses, "pinned = 1")
+		} else {
+			whereClauses = append(whereClauses, "(pinned = 0 OR pinned IS NULL)")
+		}
+	}
+
+	// Template filtering
+	if filter.IsTemplate != nil {
+		if *filter.IsTemplate {
+			whereClauses = append(whereClauses, "is_template = 1")
+		} else {
+			whereClauses = append(whereClauses, "(is_template = 0 OR is_template IS NULL)")
+		}
+	}
+
+	// Parent filtering
+	if filter.ParentID != nil {
+		whereClauses = append(whereClauses, "id IN (SELECT issue_id FROM dependencies WHERE type = 'parent-child' AND depends_on_id = ?)")
+		args = append(args, *filter.ParentID)
+	}
+
+	// Molecule type filtering
+	if filter.MolType != nil {
+		whereClauses = append(whereClauses, "mol_type = ?")
+		args = append(args, string(*filter.MolType))
+	}
+
+	// Time-based scheduling filters
+	if filter.Deferred {
+		whereClauses = append(whereClauses, "defer_until IS NOT NULL")
+	}
+	if filter.Overdue {
+		whereClauses = append(whereClauses, "due_at IS NOT NULL AND due_at < ? AND status != ?")
+		args = append(args, time.Now().Format(time.RFC3339), types.StatusClosed)
+	}
+
+	whereSQL := ""
+	if len(whereClauses) > 0 {
+		whereSQL = "WHERE " + strings.Join(whereClauses, " AND ")
+	}
+
+	limitSQL := ""
+	if filter.Limit > 0 {
+		limitSQL = fmt.Sprintf(" LIMIT %d", filter.Limit)
+	}
+
+	querySQL := fmt.Sprintf(`
+		SELECT id FROM issues
+		%s
+		ORDER BY priority ASC, created_at DESC
+		%s
+	`, whereSQL, limitSQL)
+
+	rows, err := s.db.QueryContext(ctx, querySQL, args...)
+	if err != nil {
+		return nil, fmt.Errorf("failed to search issues: %w", err)
+	}
+	defer rows.Close()
+
+	return s.scanIssueIDs(ctx, rows)
+}
+
+// GetReadyWork returns issues that are ready to work on (not blocked)
+func (s *DoltStore) GetReadyWork(ctx context.Context, filter types.WorkFilter) ([]*types.Issue, error) {
+	s.mu.RLock()
+	defer s.mu.RUnlock()
+
+	whereClauses := []string{"status = 'open'", "(ephemeral = 0 OR ephemeral IS NULL)"}
+	args := []interface{}{}
+
+	if filter.Priority != nil {
+		whereClauses = append(whereClauses, "priority = ?")
+		args = append(args, *filter.Priority)
+	}
+	if filter.Type != "" {
+		whereClauses = append(whereClauses, "issue_type = ?")
+		args = append(args, filter.Type)
+	}
+	if filter.Assignee != nil {
+		whereClauses = append(whereClauses, "assignee = ?")
+		args = append(args, *filter.Assignee)
+	}
+	if len(filter.Labels) > 0 {
+		for _, label := range filter.Labels {
+			whereClauses = append(whereClauses, "id IN (SELECT issue_id FROM labels WHERE label = ?)")
+			args = append(args, label)
+		}
+	}
+
+	// Exclude blocked issues using subquery
+	whereClauses = append(whereClauses, `
+		id NOT IN (
+			SELECT DISTINCT d.issue_id
+			FROM dependencies d
+			JOIN issues blocker ON d.depends_on_id = blocker.id
+			WHERE d.type = 'blocks'
+			  AND blocker.status IN ('open', 'in_progress', 'blocked', 'deferred', 'hooked')
+		)
+	`)
+
+	whereSQL := "WHERE " + strings.Join(whereClauses, " AND ")
+
+	limitSQL := ""
+	if filter.Limit > 0 {
+		limitSQL = fmt.Sprintf(" LIMIT %d", filter.Limit)
+	}
+
+	query := fmt.Sprintf(`
+		SELECT id FROM issues
+		%s
+		ORDER BY priority ASC, created_at DESC
+		%s
+	`, whereSQL, limitSQL)
+
+	rows, err := s.db.QueryContext(ctx, query, args...)
+	if err != nil {
+		return nil, fmt.Errorf("failed to get ready work: %w", err)
+	}
+	defer rows.Close()
+
+	return s.scanIssueIDs(ctx, rows)
+}
+
+// GetBlockedIssues returns issues that are blocked by other issues
+func (s *DoltStore) GetBlockedIssues(ctx context.Context, filter types.WorkFilter) ([]*types.BlockedIssue, error) {
+	s.mu.RLock()
+	defer s.mu.RUnlock()
+
+	rows, err := s.db.QueryContext(ctx, `
+		SELECT i.id, COUNT(d.depends_on_id) as blocked_by_count
+		FROM issues i
+		JOIN dependencies d ON i.id = d.issue_id
+		JOIN issues blocker ON d.depends_on_id = blocker.id
+		WHERE i.status IN ('open', 'in_progress', 'blocked', 'deferred', 'hooked')
+		  AND d.type = 'blocks'
+		  AND blocker.status IN ('open', 'in_progress', 'blocked', 'deferred', 'hooked')
+		GROUP BY i.id
+		ORDER BY i.priority ASC, i.created_at DESC
+	`)
+	if err != nil {
+		return nil, fmt.Errorf("failed to get blocked issues: %w", err)
+	}
+	defer rows.Close()
+
+	var results []*types.BlockedIssue
+	for rows.Next() {
+		var id string
+		var count int
+		if err := rows.Scan(&id, &count); err != nil {
+			return nil, err
+		}
+
+		issue, err := s.GetIssue(ctx, id)
+		if err != nil || issue == nil {
+			continue
+		}
+
+		// Get blocker IDs
+		var blockerIDs []string
+		blockerRows, err := s.db.QueryContext(ctx, `
+			SELECT d.depends_on_id
+			FROM dependencies d
+			JOIN issues blocker ON d.depends_on_id = blocker.id
+			WHERE d.issue_id = ?
+			  AND d.type = 'blocks'
+			  AND blocker.status IN ('open', 'in_progress', 'blocked', 'deferred', 'hooked')
+		`, id)
+		if err != nil {
+			return nil, err
+		}
+		for blockerRows.Next() {
+			var blockerID string
+			if err := blockerRows.Scan(&blockerID); err != nil {
+				blockerRows.Close()
+				return nil, err
+			}
+			blockerIDs = append(blockerIDs, blockerID)
+		}
+		blockerRows.Close()
+
+		results = append(results, &types.BlockedIssue{
+			Issue:          *issue,
+			BlockedByCount: count,
+			BlockedBy:      blockerIDs,
+		})
+	}
+
+	return results, rows.Err()
+}
+
+// GetEpicsEligibleForClosure returns epics whose children are all closed
+func (s *DoltStore) GetEpicsEligibleForClosure(ctx context.Context) ([]*types.EpicStatus, error) {
+	rows, err := s.db.QueryContext(ctx, `
+		SELECT e.id,
+		       (SELECT COUNT(*) FROM dependencies d JOIN issues c ON d.issue_id = c.id
+		        WHERE d.depends_on_id = e.id AND d.type = 'parent-child') as total_children,
+		       (SELECT COUNT(*) FROM dependencies d JOIN issues c ON d.issue_id = c.id
+		        WHERE d.depends_on_id = e.id AND d.type = 'parent-child' AND c.status = 'closed') as closed_children
+		FROM issues e
+		WHERE e.issue_type = 'epic'
+		  AND e.status != 'closed'
+		  AND e.status != 'tombstone'
+		HAVING total_children > 0 AND total_children = closed_children
+	`)
+	if err != nil {
+		return nil, fmt.Errorf("failed to get epics eligible for closure: %w", err)
+	}
+	defer rows.Close()
+
+	var results []*types.EpicStatus
+	for rows.Next() {
+		var id string
+		var total, closed int
+		if err := rows.Scan(&id, &total, &closed); err != nil {
+			return nil, err
+		}
+
+		issue, err := s.GetIssue(ctx, id)
+		if err != nil || issue == nil {
+			continue
+		}
+
+		results = append(results, &types.EpicStatus{
+			Epic:             issue,
+			TotalChildren:    total,
+			ClosedChildren:   closed,
+			EligibleForClose: total > 0 && total == closed,
+		})
+	}
+
+	return results, rows.Err()
+}
+
+// GetStaleIssues returns issues that haven't been updated recently
+func (s *DoltStore) GetStaleIssues(ctx context.Context, filter types.StaleFilter) ([]*types.Issue, error) {
+	cutoff := time.Now().AddDate(0, 0, -filter.Days)
+
+	statusClause := "status IN ('open', 'in_progress')"
+	if filter.Status != "" {
+		statusClause = "status = ?"
+	}
+
+	query := fmt.Sprintf(`
+		SELECT id FROM issues
+		WHERE updated_at < ?
+		  AND %s
+		  AND (ephemeral = 0 OR ephemeral IS NULL)
+		ORDER BY updated_at ASC
+	`, statusClause)
+	args := []interface{}{cutoff}
+	if filter.Status != "" {
+		args = append(args, filter.Status)
+	}
+
+	if filter.Limit > 0 {
+		query += fmt.Sprintf(" LIMIT %d", filter.Limit)
+	}
+
+	rows, err := s.db.QueryContext(ctx, query, args...)
+	if err != nil {
+		return nil, fmt.Errorf("failed to get stale issues: %w", err)
+	}
+	defer rows.Close()
+
+	return s.scanIssueIDs(ctx, rows)
+}
+
+// GetStatistics returns summary statistics
+func (s *DoltStore) GetStatistics(ctx context.Context) (*types.Statistics, error) {
+	stats := &types.Statistics{}
+
+	// Count by status
+	err := s.db.QueryRowContext(ctx, `
+		SELECT
+			COUNT(*) as total,
+			SUM(CASE WHEN status = 'open' THEN 1 ELSE 0 END) as open_count,
+			SUM(CASE WHEN status = 'in_progress' THEN 1 ELSE 0 END) as in_progress,
+			SUM(CASE WHEN status = 'closed' THEN 1 ELSE 0 END) as closed,
+			SUM(CASE WHEN status = 'blocked' THEN 1 ELSE 0 END) as blocked,
+			SUM(CASE WHEN status = 'deferred' THEN 1 ELSE 0 END) as deferred,
+			SUM(CASE WHEN status = 'tombstone' THEN 1 ELSE 0 END) as tombstone,
+			SUM(CASE WHEN pinned = 1 THEN 1 ELSE 0 END) as pinned
+		FROM issues
+		WHERE status != 'tombstone'
+	`).Scan(
+		&stats.TotalIssues,
+		&stats.OpenIssues,
+		&stats.InProgressIssues,
+		&stats.ClosedIssues,
+		&stats.BlockedIssues,
+		&stats.DeferredIssues,
+		&stats.TombstoneIssues,
+		&stats.PinnedIssues,
+	)
+	if err != nil {
+		return nil, fmt.Errorf("failed to get statistics: %w", err)
+	}
+
+	return stats, nil
+}
+
+// GetMoleculeProgress returns progress stats for a molecule
+func (s *DoltStore) GetMoleculeProgress(ctx context.Context, moleculeID string) (*types.MoleculeProgressStats, error) {
+	stats := &types.MoleculeProgressStats{
+		MoleculeID: moleculeID,
+	}
+
+	// Get molecule title
+	var title sql.NullString
+	err := s.db.QueryRowContext(ctx, "SELECT title FROM issues WHERE id = ?", moleculeID).Scan(&title)
+	if err == nil && title.Valid {
+		stats.MoleculeTitle = title.String
+	}
+
+	err = s.db.QueryRowContext(ctx, `
+		SELECT
+			COUNT(*) as total,
+			SUM(CASE WHEN status = 'closed' THEN 1 ELSE 0 END) as completed,
+			SUM(CASE WHEN status = 'in_progress' THEN 1 ELSE 0 END) as in_progress
+		FROM issues i
+		JOIN dependencies d ON i.id = d.issue_id
+		WHERE d.depends_on_id = ?
+		  AND d.type = 'parent-child'
+	`, moleculeID).Scan(&stats.Total, &stats.Completed, &stats.InProgress)
+
+	if err != nil {
+		return nil, fmt.Errorf("failed to get molecule progress: %w", err)
+	}
+
+	// Get first in_progress step ID
+	var stepID sql.NullString
+	_ = s.db.QueryRowContext(ctx, `
+		SELECT i.id FROM issues i
+		JOIN dependencies d ON i.id = d.issue_id
+		WHERE d.depends_on_id = ?
+		  AND d.type = 'parent-child'
+		  AND i.status = 'in_progress'
+		ORDER BY i.created_at ASC
+		LIMIT 1
+	`, moleculeID).Scan(&stepID)
+	if stepID.Valid {
+		stats.CurrentStepID = stepID.String
+	}
+
+	return stats, nil
+}
+
+// GetNextChildID returns the next available child ID for a parent
+func (s *DoltStore) GetNextChildID(ctx context.Context, parentID string) (string, error) {
+	tx, err := s.db.BeginTx(ctx, nil)
+	if err != nil {
+		return "", err
+	}
+	defer tx.Rollback()
+
+	// Get or create counter
+	var lastChild int
+	err = tx.QueryRowContext(ctx, "SELECT last_child FROM child_counters WHERE parent_id = ?", parentID).Scan(&lastChild)
+	if err == sql.ErrNoRows {
+		lastChild = 0
+	} else if err != nil {
+		return "", err
+	}
+
+	nextChild := lastChild + 1
+
+	_, err = tx.ExecContext(ctx, `
+		INSERT INTO child_counters (parent_id, last_child) VALUES (?, ?)
+		ON DUPLICATE KEY UPDATE last_child = ?
+	`, parentID, nextChild, nextChild)
+	if err != nil {
+		return "", err
+	}
+
+	if err := tx.Commit(); err != nil {
+		return "", err
+	}
+
+	return fmt.Sprintf("%s.%d", parentID, nextChild), nil
+}

internal/storage/dolt/rename.go

@@ -0,0 +1,129 @@
+package dolt
+
+import (
+	"context"
+	"fmt"
+	"time"
+
+	"github.com/steveyegge/beads/internal/types"
+)
+
+// UpdateIssueID updates an issue ID and all its references
+func (s *DoltStore) UpdateIssueID(ctx context.Context, oldID, newID string, issue *types.Issue, actor string) error {
+	tx, err := s.db.BeginTx(ctx, nil)
+	if err != nil {
+		return fmt.Errorf("failed to begin transaction: %w", err)
+	}
+	defer func() { _ = tx.Rollback() }()
+
+	// Update the issue itself
+	result, err := tx.ExecContext(ctx, `
+		UPDATE issues
+		SET id = ?, title = ?, description = ?, design = ?, acceptance_criteria = ?, notes = ?, updated_at = ?
+		WHERE id = ?
+	`, newID, issue.Title, issue.Description, issue.Design, issue.AcceptanceCriteria, issue.Notes, time.Now(), oldID)
+	if err != nil {
+		return fmt.Errorf("failed to update issue ID: %w", err)
+	}
+
+	rows, err := result.RowsAffected()
+	if err != nil {
+		return fmt.Errorf("failed to get rows affected: %w", err)
+	}
+	if rows == 0 {
+		return fmt.Errorf("issue not found: %s", oldID)
+	}
+
+	// Update references in dependencies
+	_, err = tx.ExecContext(ctx, `UPDATE dependencies SET issue_id = ? WHERE issue_id = ?`, newID, oldID)
+	if err != nil {
+		return fmt.Errorf("failed to update issue_id in dependencies: %w", err)
+	}
+
+	_, err = tx.ExecContext(ctx, `UPDATE dependencies SET depends_on_id = ? WHERE depends_on_id = ?`, newID, oldID)
+	if err != nil {
+		return fmt.Errorf("failed to update depends_on_id in dependencies: %w", err)
+	}
+
+	// Update references in events
+	_, err = tx.ExecContext(ctx, `UPDATE events SET issue_id = ? WHERE issue_id = ?`, newID, oldID)
+	if err != nil {
+		return fmt.Errorf("failed to update events: %w", err)
+	}
+
+	// Update references in labels
+	_, err = tx.ExecContext(ctx, `UPDATE labels SET issue_id = ? WHERE issue_id = ?`, newID, oldID)
+	if err != nil {
+		return fmt.Errorf("failed to update labels: %w", err)
+	}
+
+	// Update references in comments
+	_, err = tx.ExecContext(ctx, `UPDATE comments SET issue_id = ? WHERE issue_id = ?`, newID, oldID)
+	if err != nil {
+		return fmt.Errorf("failed to update comments: %w", err)
+	}
+
+	// Update dirty_issues
+	_, err = tx.ExecContext(ctx, `
+		INSERT INTO dirty_issues (issue_id, marked_at)
+		VALUES (?, ?)
+		ON DUPLICATE KEY UPDATE marked_at = VALUES(marked_at)
+	`, newID, time.Now())
+	if err != nil {
+		return fmt.Errorf("failed to mark issue dirty: %w", err)
+	}
+
+	// Delete old dirty entry
+	_, err = tx.ExecContext(ctx, `DELETE FROM dirty_issues WHERE issue_id = ?`, oldID)
+	if err != nil {
+		return fmt.Errorf("failed to delete old dirty entry: %w", err)
+	}
+
+	// Record rename event
+	_, err = tx.ExecContext(ctx, `
+		INSERT INTO events (issue_id, event_type, actor, old_value, new_value)
+		VALUES (?, 'renamed', ?, ?, ?)
+	`, newID, actor, oldID, newID)
+	if err != nil {
+		return fmt.Errorf("failed to record rename event: %w", err)
+	}
+
+	return tx.Commit()
+}
+
+// RenameDependencyPrefix updates the prefix in all dependency records
+func (s *DoltStore) RenameDependencyPrefix(ctx context.Context, oldPrefix, newPrefix string) error {
+	tx, err := s.db.BeginTx(ctx, nil)
+	if err != nil {
+		return fmt.Errorf("failed to begin transaction: %w", err)
+	}
+	defer func() { _ = tx.Rollback() }()
+
+	// Update issue_id column
+	_, err = tx.ExecContext(ctx, `
+		UPDATE dependencies
+		SET issue_id = CONCAT(?, SUBSTRING(issue_id, LENGTH(?) + 1))
+		WHERE issue_id LIKE CONCAT(?, '%')
+	`, newPrefix, oldPrefix, oldPrefix)
+	if err != nil {
+		return fmt.Errorf("failed to update issue_id in dependencies: %w", err)
+	}
+
+	// Update depends_on_id column
+	_, err = tx.ExecContext(ctx, `
+		UPDATE dependencies
+		SET depends_on_id = CONCAT(?, SUBSTRING(depends_on_id, LENGTH(?) + 1))
+		WHERE depends_on_id LIKE CONCAT(?, '%')
+	`, newPrefix, oldPrefix, oldPrefix)
+	if err != nil {
+		return fmt.Errorf("failed to update depends_on_id in dependencies: %w", err)
+	}
+
+	return tx.Commit()
+}
+
+// RenameCounterPrefix is a no-op with hash-based IDs
+func (s *DoltStore) RenameCounterPrefix(ctx context.Context, oldPrefix, newPrefix string) error {
+	// Hash-based IDs don't use counters
+	return nil
+}

internal/storage/dolt/schema.go

@@ -0,0 +1,267 @@
+package dolt
+
+// schema defines the MySQL-compatible database schema for Dolt.
+// This mirrors the SQLite schema but uses MySQL syntax.
+const schema = `
+-- Issues table
+CREATE TABLE IF NOT EXISTS issues (
+    id VARCHAR(255) PRIMARY KEY,
+    content_hash VARCHAR(64),
+    title VARCHAR(500) NOT NULL,
+    description TEXT NOT NULL,
+    design TEXT NOT NULL,
+    acceptance_criteria TEXT NOT NULL,
+    notes TEXT NOT NULL,
+    status VARCHAR(32) NOT NULL DEFAULT 'open',
+    priority INT NOT NULL DEFAULT 2,
+    issue_type VARCHAR(32) NOT NULL DEFAULT 'task',
+    assignee VARCHAR(255),
+    estimated_minutes INT,
+    created_at DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP,
+    created_by VARCHAR(255) DEFAULT '',
+    owner VARCHAR(255) DEFAULT '',
+    updated_at DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP,
+    closed_at DATETIME,
+    closed_by_session VARCHAR(255) DEFAULT '',
+    external_ref VARCHAR(255),
+    compaction_level INT DEFAULT 0,
+    compacted_at DATETIME,
+    compacted_at_commit VARCHAR(64),
+    original_size INT,
+    deleted_at DATETIME,
+    deleted_by VARCHAR(255) DEFAULT '',
+    delete_reason TEXT DEFAULT '',
+    original_type VARCHAR(32) DEFAULT '',
+    -- Messaging fields
+    sender VARCHAR(255) DEFAULT '',
+    ephemeral TINYINT(1) DEFAULT 0,
+    -- Pinned field
+    pinned TINYINT(1) DEFAULT 0,
+    -- Template field
+    is_template TINYINT(1) DEFAULT 0,
+    -- Work economics field (HOP Decision 006)
+    crystallizes TINYINT(1) DEFAULT 0,
+    -- Molecule type field
+    mol_type VARCHAR(32) DEFAULT '',
+    -- Work type field (Decision 006: mutex vs open_competition)
+    work_type VARCHAR(32) DEFAULT 'mutex',
+    -- HOP quality score field (0.0-1.0)
+    quality_score DOUBLE,
+    -- Federation source system field
+    source_system VARCHAR(255) DEFAULT '',
+    -- Source repo for multi-repo
+    source_repo VARCHAR(512) DEFAULT '',
+    -- Close reason
+    close_reason TEXT DEFAULT '',
+    -- Event fields
+    event_kind VARCHAR(32) DEFAULT '',
+    actor VARCHAR(255) DEFAULT '',
+    target VARCHAR(255) DEFAULT '',
+    payload TEXT DEFAULT '',
+    -- Gate fields
+    await_type VARCHAR(32) DEFAULT '',
+    await_id VARCHAR(255) DEFAULT '',
+    timeout_ns BIGINT DEFAULT 0,
+    waiters TEXT DEFAULT '',
+    -- Agent fields
+    hook_bead VARCHAR(255) DEFAULT '',
+    role_bead VARCHAR(255) DEFAULT '',
+    agent_state VARCHAR(32) DEFAULT '',
+    last_activity DATETIME,
+    role_type VARCHAR(32) DEFAULT '',
+    rig VARCHAR(255) DEFAULT '',
+    -- Time-based scheduling fields
+    due_at DATETIME,
+    defer_until DATETIME,
+    INDEX idx_issues_status (status),
+    INDEX idx_issues_priority (priority),
+    INDEX idx_issues_assignee (assignee),
+    INDEX idx_issues_created_at (created_at),
+    INDEX idx_issues_external_ref (external_ref)
+);
+
+-- Dependencies table (edge schema)
+CREATE TABLE IF NOT EXISTS dependencies (
+    issue_id VARCHAR(255) NOT NULL,
+    depends_on_id VARCHAR(255) NOT NULL,
+    type VARCHAR(32) NOT NULL DEFAULT 'blocks',
+    created_at DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP,
+    created_by VARCHAR(255) NOT NULL,
+    metadata JSON DEFAULT (JSON_OBJECT()),
+    thread_id VARCHAR(255) DEFAULT '',
+    PRIMARY KEY (issue_id, depends_on_id),
+    INDEX idx_dependencies_issue (issue_id),
+    INDEX idx_dependencies_depends_on (depends_on_id),
+    INDEX idx_dependencies_depends_on_type (depends_on_id, type),
+    INDEX idx_dependencies_thread (thread_id),
+    CONSTRAINT fk_dep_issue FOREIGN KEY (issue_id) REFERENCES issues(id) ON DELETE CASCADE,
+    CONSTRAINT fk_dep_depends_on FOREIGN KEY (depends_on_id) REFERENCES issues(id) ON DELETE CASCADE
+);
+
+-- Labels table
+CREATE TABLE IF NOT EXISTS labels (
+    issue_id VARCHAR(255) NOT NULL,
+    label VARCHAR(255) NOT NULL,
+    PRIMARY KEY (issue_id, label),
+    INDEX idx_labels_label (label),
+    CONSTRAINT fk_labels_issue FOREIGN KEY (issue_id) REFERENCES issues(id) ON DELETE CASCADE
+);
+
+-- Comments table
+CREATE TABLE IF NOT EXISTS comments (
+    id BIGINT AUTO_INCREMENT PRIMARY KEY,
+    issue_id VARCHAR(255) NOT NULL,
+    author VARCHAR(255) NOT NULL,
+    text TEXT NOT NULL,
+    created_at DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP,
+    INDEX idx_comments_issue (issue_id),
+    INDEX idx_comments_created_at (created_at),
+    CONSTRAINT fk_comments_issue FOREIGN KEY (issue_id) REFERENCES issues(id) ON DELETE CASCADE
+);
+
+-- Events table (audit trail)
+CREATE TABLE IF NOT EXISTS events (
+    id BIGINT AUTO_INCREMENT PRIMARY KEY,
+    issue_id VARCHAR(255) NOT NULL,
+    event_type VARCHAR(32) NOT NULL,
+    actor VARCHAR(255) NOT NULL,
+    old_value TEXT,
+    new_value TEXT,
+    comment TEXT,
+    created_at DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP,
+    INDEX idx_events_issue (issue_id),
+    INDEX idx_events_created_at (created_at),
+    CONSTRAINT fk_events_issue FOREIGN KEY (issue_id) REFERENCES issues(id) ON DELETE CASCADE
+);
+
+-- Config table
+CREATE TABLE IF NOT EXISTS config (
+    ` + "`key`" + ` VARCHAR(255) PRIMARY KEY,
+    value TEXT NOT NULL
+);
+
+-- Metadata table
+CREATE TABLE IF NOT EXISTS metadata (
+    ` + "`key`" + ` VARCHAR(255) PRIMARY KEY,
+    value TEXT NOT NULL
+);
+
+-- Dirty issues table (for incremental export)
+CREATE TABLE IF NOT EXISTS dirty_issues (
+    issue_id VARCHAR(255) PRIMARY KEY,
+    marked_at DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP,
+    INDEX idx_dirty_issues_marked_at (marked_at),
+    CONSTRAINT fk_dirty_issue FOREIGN KEY (issue_id) REFERENCES issues(id) ON DELETE CASCADE
+);
+
+-- Export hashes table
+CREATE TABLE IF NOT EXISTS export_hashes (
+    issue_id VARCHAR(255) PRIMARY KEY,
+    content_hash VARCHAR(64) NOT NULL,
+    exported_at DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP,
+    CONSTRAINT fk_export_issue FOREIGN KEY (issue_id) REFERENCES issues(id) ON DELETE CASCADE
+);
+
+-- Child counters table
+CREATE TABLE IF NOT EXISTS child_counters (
+    parent_id VARCHAR(255) PRIMARY KEY,
+    last_child INT NOT NULL DEFAULT 0,
+    CONSTRAINT fk_counter_parent FOREIGN KEY (parent_id) REFERENCES issues(id) ON DELETE CASCADE
+);
+
+-- Issue snapshots table (for compaction)
+CREATE TABLE IF NOT EXISTS issue_snapshots (
+    id BIGINT AUTO_INCREMENT PRIMARY KEY,
+    issue_id VARCHAR(255) NOT NULL,
+    snapshot_time DATETIME NOT NULL,
+    compaction_level INT NOT NULL,
+    original_size INT NOT NULL,
+    compressed_size INT NOT NULL,
+    original_content TEXT NOT NULL,
+    archived_events TEXT,
+    INDEX idx_snapshots_issue (issue_id),
+    INDEX idx_snapshots_level (compaction_level),
+    CONSTRAINT fk_snapshots_issue FOREIGN KEY (issue_id) REFERENCES issues(id) ON DELETE CASCADE
+);
+
+-- Compaction snapshots table
+CREATE TABLE IF NOT EXISTS compaction_snapshots (
+    id BIGINT AUTO_INCREMENT PRIMARY KEY,
+    issue_id VARCHAR(255) NOT NULL,
+    compaction_level INT NOT NULL,
+    snapshot_json BLOB NOT NULL,
+    created_at DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP,
+    INDEX idx_comp_snap_issue (issue_id, compaction_level, created_at DESC),
+    CONSTRAINT fk_comp_snap_issue FOREIGN KEY (issue_id) REFERENCES issues(id) ON DELETE CASCADE
+);
+
+-- Repository mtimes table (for multi-repo)
+CREATE TABLE IF NOT EXISTS repo_mtimes (
+    repo_path VARCHAR(512) PRIMARY KEY,
+    jsonl_path VARCHAR(512) NOT NULL,
+    mtime_ns BIGINT NOT NULL,
+    last_checked DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP,
+    INDEX idx_repo_mtimes_checked (last_checked)
+);
+`
+
+// defaultConfig contains the default configuration values
+const defaultConfig = `
+INSERT IGNORE INTO config (` + "`key`" + `, value) VALUES
+    ('compaction_enabled', 'false'),
+    ('compact_tier1_days', '30'),
+    ('compact_tier1_dep_levels', '2'),
+    ('compact_tier2_days', '90'),
+    ('compact_tier2_dep_levels', '5'),
+    ('compact_tier2_commits', '100'),
+    ('compact_model', 'claude-3-5-haiku-20241022'),
+    ('compact_batch_size', '50'),
+    ('compact_parallel_workers', '5'),
+    ('auto_compact_enabled', 'false');
+`
+
+// readyIssuesView is a MySQL-compatible view for ready work
+// Note: Dolt supports recursive CTEs like SQLite
+const readyIssuesView = `
+CREATE OR REPLACE VIEW ready_issues AS
+WITH RECURSIVE
+  blocked_directly AS (
+    SELECT DISTINCT d.issue_id
+    FROM dependencies d
+    JOIN issues blocker ON d.depends_on_id = blocker.id
+    WHERE d.type = 'blocks'
+      AND blocker.status IN ('open', 'in_progress', 'blocked', 'deferred', 'hooked')
+  ),
+  blocked_transitively AS (
+    SELECT issue_id, 0 as depth
+    FROM blocked_directly
+    UNION ALL
+    SELECT d.issue_id, bt.depth + 1
+    FROM blocked_transitively bt
+    JOIN dependencies d ON d.depends_on_id = bt.issue_id
+    WHERE d.type = 'parent-child'
+      AND bt.depth < 50
+  )
+SELECT i.*
+FROM issues i
+WHERE i.status = 'open'
+  AND (i.ephemeral = 0 OR i.ephemeral IS NULL)
+  AND NOT EXISTS (
+    SELECT 1 FROM blocked_transitively WHERE issue_id = i.id
+  );
+`
+
+// blockedIssuesView is a MySQL-compatible view for blocked issues
+const blockedIssuesView = `
+CREATE OR REPLACE VIEW blocked_issues AS
+SELECT
+    i.*,
+    COUNT(d.depends_on_id) as blocked_by_count
+FROM issues i
+JOIN dependencies d ON i.id = d.issue_id
+JOIN issues blocker ON d.depends_on_id = blocker.id
+WHERE i.status IN ('open', 'in_progress', 'blocked', 'deferred', 'hooked')
+  AND d.type = 'blocks'
+  AND blocker.status IN ('open', 'in_progress', 'blocked', 'deferred', 'hooked')
+GROUP BY i.id;
+`

internal/storage/dolt/store.go

@@ -0,0 +1,344 @@
+// Package dolt implements the storage interface using Dolt (versioned MySQL-compatible database).
+//
+// Dolt provides native version control for SQL data with cell-level merge, history queries,
+// and federation via Dolt remotes. This backend eliminates the need for JSONL sync layers
+// by making the database itself version-controlled.
+//
+// Key differences from SQLite backend:
+//   - Uses github.com/dolthub/driver for embedded Dolt access
+//   - Supports version control operations (commit, push, pull, branch, merge)
+//   - History queries via AS OF and dolt_history_* tables
+//   - Cell-level merge instead of line-level JSONL merge
+//
+// Connection modes:
+//   - Embedded: No server required, database/sql interface via dolthub/driver
+//   - Server: Connect to running dolt sql-server for multi-writer scenarios
+package dolt
+
+import (
+	"context"
+	"database/sql"
+	"fmt"
+	"os"
+	"path/filepath"
+	"sync"
+	"sync/atomic"
+	"time"
+
+	// Import Dolt driver
+	_ "github.com/dolthub/driver"
+)
+
+// DoltStore implements the Storage interface using Dolt
+type DoltStore struct {
+	db          *sql.DB
+	dbPath      string       // Path to Dolt database directory
+	closed      atomic.Bool  // Tracks whether Close() has been called
+	connStr     string       // Connection string for reconnection
+	mu          sync.RWMutex // Protects concurrent access
+	readOnly    bool         // True if opened in read-only mode
+
+	// Version control config
+	committerName  string
+	committerEmail string
+	remote         string // Default remote for push/pull
+	branch         string // Current branch
+}
+
+// Config holds Dolt database configuration
+type Config struct {
+	Path           string // Path to Dolt database directory
+	CommitterName  string // Git-style committer name
+	CommitterEmail string // Git-style committer email
+	Remote         string // Default remote name (e.g., "origin")
+	Database       string // Database name within Dolt (default: "beads")
+}
+
+// New creates a new Dolt storage backend
+func New(ctx context.Context, cfg *Config) (*DoltStore, error) {
+	if cfg.Path == "" {
+		return nil, fmt.Errorf("database path is required")
+	}
+
+	// Default values
+	if cfg.Database == "" {
+		cfg.Database = "beads"
+	}
+	if cfg.CommitterName == "" {
+		cfg.CommitterName = os.Getenv("GIT_AUTHOR_NAME")
+		if cfg.CommitterName == "" {
+			cfg.CommitterName = "beads"
+		}
+	}
+	if cfg.CommitterEmail == "" {
+		cfg.CommitterEmail = os.Getenv("GIT_AUTHOR_EMAIL")
+		if cfg.CommitterEmail == "" {
+			cfg.CommitterEmail = "beads@local"
+		}
+	}
+	if cfg.Remote == "" {
+		cfg.Remote = "origin"
+	}
+
+	// Ensure directory exists
+	if err := os.MkdirAll(cfg.Path, 0o750); err != nil {
+		return nil, fmt.Errorf("failed to create database directory: %w", err)
+	}
+
+	// Build Dolt connection string
+	// Format: file:///path/to/db?commitname=Name&commitemail=email&database=dbname
+	connStr := fmt.Sprintf(
+		"file://%s?commitname=%s&commitemail=%s&database=%s",
+		cfg.Path, cfg.CommitterName, cfg.CommitterEmail, cfg.Database)
+
+	db, err := sql.Open("dolt", connStr)
+	if err != nil {
+		return nil, fmt.Errorf("failed to open Dolt database: %w", err)
+	}
+
+	// Configure connection pool
+	// Dolt embedded mode is single-writer like SQLite
+	db.SetMaxOpenConns(1)
+	db.SetMaxIdleConns(1)
+	db.SetConnMaxLifetime(0)
+
+	// Test connection
+	if err := db.PingContext(ctx); err != nil {
+		return nil, fmt.Errorf("failed to ping Dolt database: %w", err)
+	}
+
+	// Convert to absolute path
+	absPath, err := filepath.Abs(cfg.Path)
+	if err != nil {
+		return nil, fmt.Errorf("failed to get absolute path: %w", err)
+	}
+
+	store := &DoltStore{
+		db:             db,
+		dbPath:         absPath,
+		connStr:        connStr,
+		committerName:  cfg.CommitterName,
+		committerEmail: cfg.CommitterEmail,
+		remote:         cfg.Remote,
+		branch:         "main",
+	}
+
+	// Initialize schema
+	if err := store.initSchema(ctx); err != nil {
+		return nil, fmt.Errorf("failed to initialize schema: %w", err)
+	}
+
+	return store, nil
+}
+
+// initSchema creates all tables if they don't exist
+func (s *DoltStore) initSchema(ctx context.Context) error {
+	// Execute schema creation
+	if _, err := s.db.ExecContext(ctx, schema); err != nil {
+		return fmt.Errorf("failed to create schema: %w", err)
+	}
+
+	// Insert default config values
+	if _, err := s.db.ExecContext(ctx, defaultConfig); err != nil {
+		return fmt.Errorf("failed to insert default config: %w", err)
+	}
+
+	// Create views
+	if _, err := s.db.ExecContext(ctx, readyIssuesView); err != nil {
+		return fmt.Errorf("failed to create ready_issues view: %w", err)
+	}
+	if _, err := s.db.ExecContext(ctx, blockedIssuesView); err != nil {
+		return fmt.Errorf("failed to create blocked_issues view: %w", err)
+	}
+
+	return nil
+}
+
+// Close closes the database connection
+func (s *DoltStore) Close() error {
+	s.closed.Store(true)
+	s.mu.Lock()
+	defer s.mu.Unlock()
+	return s.db.Close()
+}
+
+// Path returns the database directory path
+func (s *DoltStore) Path() string {
+	return s.dbPath
+}
+
+// IsClosed returns true if Close() has been called
+func (s *DoltStore) IsClosed() bool {
+	return s.closed.Load()
+}
+
+// UnderlyingDB returns the underlying *sql.DB connection
+func (s *DoltStore) UnderlyingDB() *sql.DB {
+	return s.db
+}
+
+// UnderlyingConn returns a connection from the pool
+func (s *DoltStore) UnderlyingConn(ctx context.Context) (*sql.Conn, error) {
+	return s.db.Conn(ctx)
+}
+
+// =============================================================================
+// Version Control Operations (Dolt-specific extensions)
+// =============================================================================
+
+// Commit creates a Dolt commit with the given message
+func (s *DoltStore) Commit(ctx context.Context, message string) error {
+	_, err := s.db.ExecContext(ctx, "CALL DOLT_COMMIT('-Am', ?)", message)
+	if err != nil {
+		return fmt.Errorf("failed to commit: %w", err)
+	}
+	return nil
+}
+
+// Push pushes commits to the remote
+func (s *DoltStore) Push(ctx context.Context) error {
+	_, err := s.db.ExecContext(ctx, "CALL DOLT_PUSH(?, ?)", s.remote, s.branch)
+	if err != nil {
+		return fmt.Errorf("failed to push to %s/%s: %w", s.remote, s.branch, err)
+	}
+	return nil
+}
+
+// Pull pulls changes from the remote
+func (s *DoltStore) Pull(ctx context.Context) error {
+	_, err := s.db.ExecContext(ctx, "CALL DOLT_PULL(?)", s.remote)
+	if err != nil {
+		return fmt.Errorf("failed to pull from %s: %w", s.remote, err)
+	}
+	return nil
+}
+
+// Branch creates a new branch
+func (s *DoltStore) Branch(ctx context.Context, name string) error {
+	_, err := s.db.ExecContext(ctx, "CALL DOLT_BRANCH(?)", name)
+	if err != nil {
+		return fmt.Errorf("failed to create branch %s: %w", name, err)
+	}
+	return nil
+}
+
+// Checkout switches to the specified branch
+func (s *DoltStore) Checkout(ctx context.Context, branch string) error {
+	_, err := s.db.ExecContext(ctx, "CALL DOLT_CHECKOUT(?)", branch)
+	if err != nil {
+		return fmt.Errorf("failed to checkout branch %s: %w", branch, err)
+	}
+	s.branch = branch
+	return nil
+}
+
+// Merge merges the specified branch into the current branch
+func (s *DoltStore) Merge(ctx context.Context, branch string) error {
+	_, err := s.db.ExecContext(ctx, "CALL DOLT_MERGE(?)", branch)
+	if err != nil {
+		return fmt.Errorf("failed to merge branch %s: %w", branch, err)
+	}
+	return nil
+}
+
+// CurrentBranch returns the current branch name
+func (s *DoltStore) CurrentBranch(ctx context.Context) (string, error) {
+	var branch string
+	err := s.db.QueryRowContext(ctx, "SELECT active_branch()").Scan(&branch)
+	if err != nil {
+		return "", fmt.Errorf("failed to get current branch: %w", err)
+	}
+	return branch, nil
+}
+
+// Log returns recent commit history
+func (s *DoltStore) Log(ctx context.Context, limit int) ([]CommitInfo, error) {
+	rows, err := s.db.QueryContext(ctx, `
+		SELECT commit_hash, committer, email, date, message
+		FROM dolt_log
+		LIMIT ?
+	`, limit)
+	if err != nil {
+		return nil, fmt.Errorf("failed to get log: %w", err)
+	}
+	defer rows.Close()
+
+	var commits []CommitInfo
+	for rows.Next() {
+		var c CommitInfo
+		if err := rows.Scan(&c.Hash, &c.Author, &c.Email, &c.Date, &c.Message); err != nil {
+			return nil, fmt.Errorf("failed to scan commit: %w", err)
+		}
+		commits = append(commits, c)
+	}
+	return commits, rows.Err()
+}
+
+// CommitInfo represents a Dolt commit
+type CommitInfo struct {
+	Hash    string
+	Author  string
+	Email   string
+	Date    time.Time
+	Message string
+}
+
+// HistoryEntry represents a row from dolt_history_* table
+type HistoryEntry struct {
+	CommitHash string
+	Committer  string
+	CommitDate time.Time
+	// Issue data at that commit
+	IssueData map[string]interface{}
+}
+
+// AddRemote adds a Dolt remote
+func (s *DoltStore) AddRemote(ctx context.Context, name, url string) error {
+	_, err := s.db.ExecContext(ctx, "CALL DOLT_REMOTE('add', ?, ?)", name, url)
+	if err != nil {
+		return fmt.Errorf("failed to add remote %s: %w", name, err)
+	}
+	return nil
+}
+
+// Status returns the current Dolt status (staged/unstaged changes)
+func (s *DoltStore) Status(ctx context.Context) (*DoltStatus, error) {
+	rows, err := s.db.QueryContext(ctx, "SELECT table_name, staged, status FROM dolt_status")
+	if err != nil {
+		return nil, fmt.Errorf("failed to get status: %w", err)
+	}
+	defer rows.Close()
+
+	status := &DoltStatus{
+		Staged:   make([]StatusEntry, 0),
+		Unstaged: make([]StatusEntry, 0),
+	}
+
+	for rows.Next() {
+		var tableName string
+		var staged bool
+		var statusInt int
+		if err := rows.Scan(&tableName, &staged, &statusInt); err != nil {
+			return nil, fmt.Errorf("failed to scan status: %w", err)
+		}
+		entry := StatusEntry{Table: tableName, Status: statusInt}
+		if staged {
+			status.Staged = append(status.Staged, entry)
+		} else {
+			status.Unstaged = append(status.Unstaged, entry)
+		}
+	}
+	return status, rows.Err()
+}
+
+// DoltStatus represents the current repository status
+type DoltStatus struct {
+	Staged   []StatusEntry
+	Unstaged []StatusEntry
+}
+
+// StatusEntry represents a changed table
+type StatusEntry struct {
+	Table  string
+	Status int // 1=new, 2=modified, 3=deleted
+}

internal/storage/dolt/transaction.go

@@ -0,0 +1,325 @@
+package dolt
+
+import (
+	"context"
+	"database/sql"
+	"fmt"
+	"strings"
+	"time"
+
+	"github.com/steveyegge/beads/internal/storage"
+	"github.com/steveyegge/beads/internal/types"
+)
+
+// doltTransaction implements storage.Transaction for Dolt
+type doltTransaction struct {
+	tx    *sql.Tx
+	store *DoltStore
+}
+
+// RunInTransaction executes a function within a database transaction
+func (s *DoltStore) RunInTransaction(ctx context.Context, fn func(tx storage.Transaction) error) error {
+	sqlTx, err := s.db.BeginTx(ctx, nil)
+	if err != nil {
+		return fmt.Errorf("failed to begin transaction: %w", err)
+	}
+
+	tx := &doltTransaction{tx: sqlTx, store: s}
+
+	defer func() {
+		if r := recover(); r != nil {
+			_ = sqlTx.Rollback()
+			panic(r)
+		}
+	}()
+
+	if err := fn(tx); err != nil {
+		_ = sqlTx.Rollback()
+		return err
+	}
+
+	return sqlTx.Commit()
+}
+
+// CreateIssue creates an issue within the transaction
+func (t *doltTransaction) CreateIssue(ctx context.Context, issue *types.Issue, actor string) error {
+	now := time.Now()
+	if issue.CreatedAt.IsZero() {
+		issue.CreatedAt = now
+	}
+	if issue.UpdatedAt.IsZero() {
+		issue.UpdatedAt = now
+	}
+	if issue.ContentHash == "" {
+		issue.ContentHash = issue.ComputeContentHash()
+	}
+
+	return insertIssueTx(ctx, t.tx, issue)
+}
+
+// CreateIssues creates multiple issues within the transaction
+func (t *doltTransaction) CreateIssues(ctx context.Context, issues []*types.Issue, actor string) error {
+	for _, issue := range issues {
+		if err := t.CreateIssue(ctx, issue, actor); err != nil {
+			return err
+		}
+	}
+	return nil
+}
+
+// GetIssue retrieves an issue within the transaction
+func (t *doltTransaction) GetIssue(ctx context.Context, id string) (*types.Issue, error) {
+	return scanIssueTx(ctx, t.tx, id)
+}
+
+// SearchIssues searches for issues within the transaction
+func (t *doltTransaction) SearchIssues(ctx context.Context, query string, filter types.IssueFilter) ([]*types.Issue, error) {
+	// Simplified search for transaction context
+	whereClauses := []string{}
+	args := []interface{}{}
+
+	if query != "" {
+		whereClauses = append(whereClauses, "(title LIKE ? OR description LIKE ? OR id LIKE ?)")
+		pattern := "%" + query + "%"
+		args = append(args, pattern, pattern, pattern)
+	}
+
+	if filter.Status != nil {
+		whereClauses = append(whereClauses, "status = ?")
+		args = append(args, *filter.Status)
+	}
+
+	whereSQL := ""
+	if len(whereClauses) > 0 {
+		whereSQL = "WHERE " + strings.Join(whereClauses, " AND ")
+	}
+
+	rows, err := t.tx.QueryContext(ctx, fmt.Sprintf(`
+		SELECT id FROM issues %s ORDER BY priority ASC, created_at DESC
+	`, whereSQL), args...)
+	if err != nil {
+		return nil, err
+	}
+	defer rows.Close()
+
+	var issues []*types.Issue
+	for rows.Next() {
+		var id string
+		if err := rows.Scan(&id); err != nil {
+			return nil, err
+		}
+		issue, err := t.GetIssue(ctx, id)
+		if err != nil {
+			return nil, err
+		}
+		if issue != nil {
+			issues = append(issues, issue)
+		}
+	}
+	return issues, rows.Err()
+}
+
+// UpdateIssue updates an issue within the transaction
+func (t *doltTransaction) UpdateIssue(ctx context.Context, id string, updates map[string]interface{}, actor string) error {
+	setClauses := []string{"updated_at = ?"}
+	args := []interface{}{time.Now()}
+
+	for key, value := range updates {
+		if !isAllowedUpdateField(key) {
+			return fmt.Errorf("invalid field for update: %s", key)
+		}
+		columnName := key
+		if key == "wisp" {
+			columnName = "ephemeral"
+		}
+		setClauses = append(setClauses, fmt.Sprintf("`%s` = ?", columnName))
+		args = append(args, value)
+	}
+
+	args = append(args, id)
+	query := fmt.Sprintf("UPDATE issues SET %s WHERE id = ?", strings.Join(setClauses, ", "))
+	_, err := t.tx.ExecContext(ctx, query, args...)
+	return err
+}
+
+// CloseIssue closes an issue within the transaction
+func (t *doltTransaction) CloseIssue(ctx context.Context, id string, reason string, actor string, session string) error {
+	now := time.Now()
+	_, err := t.tx.ExecContext(ctx, `
+		UPDATE issues SET status = ?, closed_at = ?, updated_at = ?, close_reason = ?, closed_by_session = ?
+		WHERE id = ?
+	`, types.StatusClosed, now, now, reason, session, id)
+	return err
+}
+
+// DeleteIssue deletes an issue within the transaction
+func (t *doltTransaction) DeleteIssue(ctx context.Context, id string) error {
+	_, err := t.tx.ExecContext(ctx, "DELETE FROM issues WHERE id = ?", id)
+	return err
+}
+
+// AddDependency adds a dependency within the transaction
+func (t *doltTransaction) AddDependency(ctx context.Context, dep *types.Dependency, actor string) error {
+	_, err := t.tx.ExecContext(ctx, `
+		INSERT INTO dependencies (issue_id, depends_on_id, type, created_at, created_by, thread_id)
+		VALUES (?, ?, ?, NOW(), ?, ?)
+		ON DUPLICATE KEY UPDATE type = VALUES(type)
+	`, dep.IssueID, dep.DependsOnID, dep.Type, actor, dep.ThreadID)
+	return err
+}
+
+// RemoveDependency removes a dependency within the transaction
+func (t *doltTransaction) RemoveDependency(ctx context.Context, issueID, dependsOnID string, actor string) error {
+	_, err := t.tx.ExecContext(ctx, `
+		DELETE FROM dependencies WHERE issue_id = ? AND depends_on_id = ?
+	`, issueID, dependsOnID)
+	return err
+}
+
+// AddLabel adds a label within the transaction
+func (t *doltTransaction) AddLabel(ctx context.Context, issueID, label, actor string) error {
+	_, err := t.tx.ExecContext(ctx, `
+		INSERT IGNORE INTO labels (issue_id, label) VALUES (?, ?)
+	`, issueID, label)
+	return err
+}
+
+// RemoveLabel removes a label within the transaction
+func (t *doltTransaction) RemoveLabel(ctx context.Context, issueID, label, actor string) error {
+	_, err := t.tx.ExecContext(ctx, `
+		DELETE FROM labels WHERE issue_id = ? AND label = ?
+	`, issueID, label)
+	return err
+}
+
+// SetConfig sets a config value within the transaction
+func (t *doltTransaction) SetConfig(ctx context.Context, key, value string) error {
+	_, err := t.tx.ExecContext(ctx, `
+		INSERT INTO config (`+"`key`"+`, value) VALUES (?, ?)
+		ON DUPLICATE KEY UPDATE value = VALUES(value)
+	`, key, value)
+	return err
+}
+
+// GetConfig gets a config value within the transaction
+func (t *doltTransaction) GetConfig(ctx context.Context, key string) (string, error) {
+	var value string
+	err := t.tx.QueryRowContext(ctx, "SELECT value FROM config WHERE `key` = ?", key).Scan(&value)
+	if err == sql.ErrNoRows {
+		return "", nil
+	}
+	return value, err
+}
+
+// SetMetadata sets a metadata value within the transaction
+func (t *doltTransaction) SetMetadata(ctx context.Context, key, value string) error {
+	_, err := t.tx.ExecContext(ctx, `
+		INSERT INTO metadata (`+"`key`"+`, value) VALUES (?, ?)
+		ON DUPLICATE KEY UPDATE value = VALUES(value)
+	`, key, value)
+	return err
+}
+
+// GetMetadata gets a metadata value within the transaction
+func (t *doltTransaction) GetMetadata(ctx context.Context, key string) (string, error) {
+	var value string
+	err := t.tx.QueryRowContext(ctx, "SELECT value FROM metadata WHERE `key` = ?", key).Scan(&value)
+	if err == sql.ErrNoRows {
+		return "", nil
+	}
+	return value, err
+}
+
+// AddComment adds a comment within the transaction
+func (t *doltTransaction) AddComment(ctx context.Context, issueID, actor, comment string) error {
+	_, err := t.tx.ExecContext(ctx, `
+		INSERT INTO events (issue_id, event_type, actor, comment)
+		VALUES (?, ?, ?, ?)
+	`, issueID, types.EventCommented, actor, comment)
+	return err
+}
+
+// Helper functions for transaction context
+
+func insertIssueTx(ctx context.Context, tx *sql.Tx, issue *types.Issue) error {
+	_, err := tx.ExecContext(ctx, `
+		INSERT INTO issues (
+			id, content_hash, title, description, design, acceptance_criteria, notes,
+			status, priority, issue_type, assignee, estimated_minutes,
+			created_at, created_by, owner, updated_at, closed_at,
+			sender, ephemeral, pinned, is_template, crystallizes
+		) VALUES (
+			?, ?, ?, ?, ?, ?, ?,
+			?, ?, ?, ?, ?,
+			?, ?, ?, ?, ?,
+			?, ?, ?, ?, ?
+		)
+	`,
+		issue.ID, issue.ContentHash, issue.Title, issue.Description, issue.Design, issue.AcceptanceCriteria, issue.Notes,
+		issue.Status, issue.Priority, issue.IssueType, nullString(issue.Assignee), nullInt(issue.EstimatedMinutes),
+		issue.CreatedAt, issue.CreatedBy, issue.Owner, issue.UpdatedAt, issue.ClosedAt,
+		issue.Sender, issue.Ephemeral, issue.Pinned, issue.IsTemplate, issue.Crystallizes,
+	)
+	return err
+}
+
+func scanIssueTx(ctx context.Context, tx *sql.Tx, id string) (*types.Issue, error) {
+	var issue types.Issue
+	var closedAt sql.NullTime
+	var estimatedMinutes sql.NullInt64
+	var assignee, owner, contentHash sql.NullString
+	var ephemeral, pinned, isTemplate, crystallizes sql.NullInt64
+
+	err := tx.QueryRowContext(ctx, `
+		SELECT id, content_hash, title, description, design, acceptance_criteria, notes,
+		       status, priority, issue_type, assignee, estimated_minutes,
+		       created_at, created_by, owner, updated_at, closed_at,
+		       ephemeral, pinned, is_template, crystallizes
+		FROM issues
+		WHERE id = ?
+	`, id).Scan(
+		&issue.ID, &contentHash, &issue.Title, &issue.Description, &issue.Design,
+		&issue.AcceptanceCriteria, &issue.Notes, &issue.Status,
+		&issue.Priority, &issue.IssueType, &assignee, &estimatedMinutes,
+		&issue.CreatedAt, &issue.CreatedBy, &owner, &issue.UpdatedAt, &closedAt,
+		&ephemeral, &pinned, &isTemplate, &crystallizes,
+	)
+
+	if err == sql.ErrNoRows {
+		return nil, nil
+	}
+	if err != nil {
+		return nil, err
+	}
+
+	if contentHash.Valid {
+		issue.ContentHash = contentHash.String
+	}
+	if closedAt.Valid {
+		issue.ClosedAt = &closedAt.Time
+	}
+	if estimatedMinutes.Valid {
+		mins := int(estimatedMinutes.Int64)
+		issue.EstimatedMinutes = &mins
+	}
+	if assignee.Valid {
+		issue.Assignee = assignee.String
+	}
+	if owner.Valid {
+		issue.Owner = owner.String
+	}
+	if ephemeral.Valid && ephemeral.Int64 != 0 {
+		issue.Ephemeral = true
+	}
+	if pinned.Valid && pinned.Int64 != 0 {
+		issue.Pinned = true
+	}
+	if isTemplate.Valid && isTemplate.Int64 != 0 {
+		issue.IsTemplate = true
+	}
+	if crystallizes.Valid && crystallizes.Int64 != 0 {
+		issue.Crystallizes = true
+	}
+
+	return &issue, nil
+}