feat(types): add template molecules infrastructure for beads-1ra

Add support for template molecules (is_template field and TypeMolecule type):

- Add IsTemplate field to Issue type with JSON support
- Add TypeMolecule constant to IssueType constants
- Add IsTemplate filter to IssueFilter for querying
- Update all SQL queries to include is_template column
- Add migration 024 for is_template column
- Add FindMoleculesJSONLInDir helper for molecules.jsonl path detection

This enables treating certain issues as read-only templates that can be
instantiated to create work items. The template flag allows separating
template molecules from regular work items in queries and exports.

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

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

internal/beads/beads.go

@@ -211,11 +211,12 @@ const (
 
 // IssueType constants
 const (
-	TypeBug     = types.TypeBug
+	TypeBug      = types.TypeBug
-	TypeFeature = types.TypeFeature
+	TypeFeature  = types.TypeFeature
-	TypeTask    = types.TypeTask
+	TypeTask     = types.TypeTask
-	TypeEpic    = types.TypeEpic
+	TypeEpic     = types.TypeEpic
-	TypeChore   = types.TypeChore
+	TypeChore    = types.TypeChore
+	TypeMolecule = types.TypeMolecule
 )
 
 // DependencyType constants

internal/storage/sqlite/dependencies.go

@@ -233,7 +233,7 @@ func (s *SQLiteStorage) GetDependenciesWithMetadata(ctx context.Context, issueID
 		       i.status, i.priority, i.issue_type, i.assignee, i.estimated_minutes,
 		       i.created_at, i.updated_at, i.closed_at, i.external_ref, i.source_repo,
 		       i.deleted_at, i.deleted_by, i.delete_reason, i.original_type,
-		       i.sender, i.ephemeral, i.pinned,
+		       i.sender, i.ephemeral, i.pinned, i.is_template,
 		       d.type
 		FROM issues i
 		JOIN dependencies d ON i.id = d.depends_on_id
@@ -255,7 +255,7 @@ func (s *SQLiteStorage) GetDependentsWithMetadata(ctx context.Context, issueID s
 		       i.status, i.priority, i.issue_type, i.assignee, i.estimated_minutes,
 		       i.created_at, i.updated_at, i.closed_at, i.external_ref, i.source_repo,
 		       i.deleted_at, i.deleted_by, i.delete_reason, i.original_type,
-		       i.sender, i.ephemeral, i.pinned,
+		       i.sender, i.ephemeral, i.pinned, i.is_template,
 		       d.type
 		FROM issues i
 		JOIN dependencies d ON i.id = d.issue_id
@@ -716,6 +716,8 @@ func (s *SQLiteStorage) scanIssues(ctx context.Context, rows *sql.Rows) ([]*type
 		var ephemeral sql.NullInt64
 		// Pinned field (bd-7h5)
 		var pinned sql.NullInt64
+		// Template field (beads-1ra)
+		var isTemplate sql.NullInt64
 
 		err := rows.Scan(
 			&issue.ID, &contentHash, &issue.Title, &issue.Description, &issue.Design,
@@ -723,7 +725,7 @@ func (s *SQLiteStorage) scanIssues(ctx context.Context, rows *sql.Rows) ([]*type
 			&issue.Priority, &issue.IssueType, &assignee, &estimatedMinutes,
 			&issue.CreatedAt, &issue.UpdatedAt, &closedAt, &externalRef, &sourceRepo, &closeReason,
 			&deletedAt, &deletedBy, &deleteReason, &originalType,
-			&sender, &ephemeral, &pinned,
+			&sender, &ephemeral, &pinned, &isTemplate,
 		)
 		if err != nil {
 			return nil, fmt.Errorf("failed to scan issue: %w", err)
@@ -772,6 +774,10 @@ func (s *SQLiteStorage) scanIssues(ctx context.Context, rows *sql.Rows) ([]*type
 		if pinned.Valid && pinned.Int64 != 0 {
 			issue.Pinned = true
 		}
+		// Template field (beads-1ra)
+		if isTemplate.Valid && isTemplate.Int64 != 0 {
+			issue.IsTemplate = true
+		}
 
 		issues = append(issues, &issue)
 		issueIDs = append(issueIDs, issue.ID)
@@ -813,6 +819,8 @@ func (s *SQLiteStorage) scanIssuesWithDependencyType(ctx context.Context, rows *
 		var ephemeral sql.NullInt64
 		// Pinned field (bd-7h5)
 		var pinned sql.NullInt64
+		// Template field (beads-1ra)
+		var isTemplate sql.NullInt64
 		var depType types.DependencyType
 
 		err := rows.Scan(
@@ -821,7 +829,7 @@ func (s *SQLiteStorage) scanIssuesWithDependencyType(ctx context.Context, rows *
 			&issue.Priority, &issue.IssueType, &assignee, &estimatedMinutes,
 			&issue.CreatedAt, &issue.UpdatedAt, &closedAt, &externalRef, &sourceRepo,
 			&deletedAt, &deletedBy, &deleteReason, &originalType,
-			&sender, &ephemeral, &pinned,
+			&sender, &ephemeral, &pinned, &isTemplate,
 			&depType,
 		)
 		if err != nil {
@@ -868,6 +876,10 @@ func (s *SQLiteStorage) scanIssuesWithDependencyType(ctx context.Context, rows *
 		if pinned.Valid && pinned.Int64 != 0 {
 			issue.Pinned = true
 		}
+		// Template field (beads-1ra)
+		if isTemplate.Valid && isTemplate.Int64 != 0 {
+			issue.IsTemplate = true
+		}
 
 		// Fetch labels for this issue
 		labels, err := s.GetLabels(ctx, issue.ID)

internal/storage/sqlite/issues.go

@@ -35,6 +35,10 @@ func insertIssue(ctx context.Context, conn *sql.Conn, issue *types.Issue) error
 	if issue.Pinned {
 		pinned = 1
 	}
+	isTemplate := 0
+	if issue.IsTemplate {
+		isTemplate = 1
+	}
 
 	_, err := conn.ExecContext(ctx, `
 		INSERT OR IGNORE INTO issues (
@@ -42,8 +46,8 @@ func insertIssue(ctx context.Context, conn *sql.Conn, issue *types.Issue) error
 			status, priority, issue_type, assignee, estimated_minutes,
 			created_at, updated_at, closed_at, external_ref, source_repo, close_reason,
 			deleted_at, deleted_by, delete_reason, original_type,
-			sender, ephemeral, pinned
+			sender, ephemeral, pinned, is_template
-		) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
+		) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
 	`,
 		issue.ID, issue.ContentHash, issue.Title, issue.Description, issue.Design,
 		issue.AcceptanceCriteria, issue.Notes, issue.Status,
@@ -51,7 +55,7 @@ func insertIssue(ctx context.Context, conn *sql.Conn, issue *types.Issue) error
 		issue.EstimatedMinutes, issue.CreatedAt, issue.UpdatedAt,
 		issue.ClosedAt, issue.ExternalRef, sourceRepo, issue.CloseReason,
 		issue.DeletedAt, issue.DeletedBy, issue.DeleteReason, issue.OriginalType,
-		issue.Sender, ephemeral, pinned,
+		issue.Sender, ephemeral, pinned, isTemplate,
 	)
 	if err != nil {
 		// INSERT OR IGNORE should handle duplicates, but driver may still return error
@@ -72,8 +76,8 @@ func insertIssues(ctx context.Context, conn *sql.Conn, issues []*types.Issue) er
 			status, priority, issue_type, assignee, estimated_minutes,
 			created_at, updated_at, closed_at, external_ref, source_repo, close_reason,
 			deleted_at, deleted_by, delete_reason, original_type,
-			sender, ephemeral, pinned
+			sender, ephemeral, pinned, is_template
-		) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
+		) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
 	`)
 	if err != nil {
 		return fmt.Errorf("failed to prepare statement: %w", err)
@@ -94,6 +98,10 @@ func insertIssues(ctx context.Context, conn *sql.Conn, issues []*types.Issue) er
 		if issue.Pinned {
 			pinned = 1
 		}
+		isTemplate := 0
+		if issue.IsTemplate {
+			isTemplate = 1
+		}
 
 		_, err = stmt.ExecContext(ctx,
 			issue.ID, issue.ContentHash, issue.Title, issue.Description, issue.Design,
@@ -102,7 +110,7 @@ func insertIssues(ctx context.Context, conn *sql.Conn, issues []*types.Issue) er
 			issue.EstimatedMinutes, issue.CreatedAt, issue.UpdatedAt,
 			issue.ClosedAt, issue.ExternalRef, sourceRepo, issue.CloseReason,
 			issue.DeletedAt, issue.DeletedBy, issue.DeleteReason, issue.OriginalType,
-			issue.Sender, ephemeral, pinned,
+			issue.Sender, ephemeral, pinned, isTemplate,
 		)
 		if err != nil {
 			// INSERT OR IGNORE should handle duplicates, but driver may still return error

internal/storage/sqlite/labels.go

@@ -159,7 +159,7 @@ func (s *SQLiteStorage) GetIssuesByLabel(ctx context.Context, label string) ([]*
 		       i.status, i.priority, i.issue_type, i.assignee, i.estimated_minutes,
 		       i.created_at, i.updated_at, i.closed_at, i.external_ref, i.source_repo, i.close_reason,
 		       i.deleted_at, i.deleted_by, i.delete_reason, i.original_type,
-		       i.sender, i.ephemeral, i.pinned
+		       i.sender, i.ephemeral, i.pinned, i.is_template
 		FROM issues i
 		JOIN labels l ON i.id = l.issue_id
 		WHERE l.label = ?

internal/storage/sqlite/migrations.go

@@ -40,6 +40,7 @@ var migrationsList = []Migration{
 	{"migrate_edge_fields", migrations.MigrateEdgeFields},
 	{"drop_edge_columns", migrations.MigrateDropEdgeColumns},
 	{"pinned_column", migrations.MigratePinnedColumn},
+	{"is_template_column", migrations.MigrateIsTemplateColumn},
 }
 
 // MigrationInfo contains metadata about a migration for inspection
@@ -87,6 +88,7 @@ func getMigrationDescription(name string) string {
 		"migrate_edge_fields":          "Migrates existing issue fields (replies_to, relates_to, duplicate_of, superseded_by) to dependency edges (Decision 004 Phase 3)",
 		"drop_edge_columns":            "Drops deprecated edge columns (replies_to, relates_to, duplicate_of, superseded_by) from issues table (Decision 004 Phase 4)",
 		"pinned_column":                "Adds pinned column for persistent context markers (bd-7h5)",
+		"is_template_column":           "Adds is_template column for template molecules (beads-1ra)",
 	}
 	
 	if desc, ok := descriptions[name]; ok {

internal/storage/sqlite/migrations/024_is_template_column.go

@@ -0,0 +1,40 @@
+package migrations
+
+import (
+	"database/sql"
+	"fmt"
+)
+
+// MigrateIsTemplateColumn adds the is_template column to the issues table.
+// Template issues (molecules) are read-only templates that should be filtered
+// from work views by default (beads-1ra).
+func MigrateIsTemplateColumn(db *sql.DB) error {
+	// Check if column already exists
+	var columnExists bool
+	err := db.QueryRow(`
+		SELECT COUNT(*) > 0
+		FROM pragma_table_info('issues')
+		WHERE name = 'is_template'
+	`).Scan(&columnExists)
+	if err != nil {
+		return fmt.Errorf("failed to check is_template column: %w", err)
+	}
+
+	if columnExists {
+		return nil
+	}
+
+	// Add the is_template column
+	_, err = db.Exec(`ALTER TABLE issues ADD COLUMN is_template INTEGER DEFAULT 0`)
+	if err != nil {
+		return fmt.Errorf("failed to add is_template column: %w", err)
+	}
+
+	// Add index for template issues (for efficient filtering)
+	_, err = db.Exec(`CREATE INDEX IF NOT EXISTS idx_issues_is_template ON issues(is_template) WHERE is_template = 1`)
+	if err != nil {
+		return fmt.Errorf("failed to create is_template index: %w", err)
+	}
+
+	return nil
+}

internal/storage/sqlite/migrations_test.go

@@ -486,13 +486,14 @@ func TestMigrateContentHashColumn(t *testing.T) {
 				sender TEXT DEFAULT '',
 				ephemeral INTEGER DEFAULT 0,
 				pinned INTEGER DEFAULT 0,
+				is_template INTEGER DEFAULT 0,
 				replies_to TEXT DEFAULT '',
 				relates_to TEXT DEFAULT '',
 				duplicate_of TEXT DEFAULT '',
 				superseded_by TEXT DEFAULT '',
 				CHECK ((status = 'closed') = (closed_at IS NOT NULL))
 			);
-			INSERT INTO issues SELECT id, title, description, design, acceptance_criteria, notes, status, priority, issue_type, assignee, estimated_minutes, created_at, updated_at, closed_at, external_ref, compaction_level, compacted_at, original_size, compacted_at_commit, source_repo, '', NULL, '', '', '', '', 0, 0, '', '', '', '' FROM issues_backup;
+			INSERT INTO issues SELECT id, title, description, design, acceptance_criteria, notes, status, priority, issue_type, assignee, estimated_minutes, created_at, updated_at, closed_at, external_ref, compaction_level, compacted_at, original_size, compacted_at_commit, source_repo, '', NULL, '', '', '', '', 0, 0, 0, '', '', '', '' FROM issues_backup;
 			DROP TABLE issues_backup;
 		`)
 		if err != nil {

internal/storage/sqlite/multirepo.go

@@ -265,6 +265,10 @@ func (s *SQLiteStorage) upsertIssueInTx(ctx context.Context, tx *sql.Tx, issue *
 	if issue.Pinned {
 		pinned = 1
 	}
+	isTemplate := 0
+	if issue.IsTemplate {
+		isTemplate = 1
+	}
 
 	if err == sql.ErrNoRows {
 		// Issue doesn't exist - insert it
@@ -274,8 +278,8 @@ func (s *SQLiteStorage) upsertIssueInTx(ctx context.Context, tx *sql.Tx, issue *
 				status, priority, issue_type, assignee, estimated_minutes,
 				created_at, updated_at, closed_at, external_ref, source_repo, close_reason,
 				deleted_at, deleted_by, delete_reason, original_type,
-				sender, ephemeral, pinned
+				sender, ephemeral, pinned, is_template
-			) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
+			) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
 		`,
 			issue.ID, issue.ContentHash, issue.Title, issue.Description, issue.Design,
 			issue.AcceptanceCriteria, issue.Notes, issue.Status,
@@ -283,7 +287,7 @@ func (s *SQLiteStorage) upsertIssueInTx(ctx context.Context, tx *sql.Tx, issue *
 			issue.EstimatedMinutes, issue.CreatedAt, issue.UpdatedAt,
 			issue.ClosedAt, issue.ExternalRef, issue.SourceRepo, issue.CloseReason,
 			issue.DeletedAt, issue.DeletedBy, issue.DeleteReason, issue.OriginalType,
-			issue.Sender, ephemeral, pinned,
+			issue.Sender, ephemeral, pinned, isTemplate,
 		)
 		if err != nil {
 			return fmt.Errorf("failed to insert issue: %w", err)
@@ -307,7 +311,7 @@ func (s *SQLiteStorage) upsertIssueInTx(ctx context.Context, tx *sql.Tx, issue *
 					issue_type = ?, assignee = ?, estimated_minutes = ?,
 					updated_at = ?, closed_at = ?, external_ref = ?, source_repo = ?,
 					deleted_at = ?, deleted_by = ?, delete_reason = ?, original_type = ?,
-					sender = ?, ephemeral = ?, pinned = ?
+					sender = ?, ephemeral = ?, pinned = ?, is_template = ?
 				WHERE id = ?
 			`,
 				issue.ContentHash, issue.Title, issue.Description, issue.Design,
@@ -315,7 +319,7 @@ func (s *SQLiteStorage) upsertIssueInTx(ctx context.Context, tx *sql.Tx, issue *
 				issue.IssueType, issue.Assignee, issue.EstimatedMinutes,
 				issue.UpdatedAt, issue.ClosedAt, issue.ExternalRef, issue.SourceRepo,
 				issue.DeletedAt, issue.DeletedBy, issue.DeleteReason, issue.OriginalType,
-				issue.Sender, ephemeral, pinned,
+				issue.Sender, ephemeral, pinned, isTemplate,
 				issue.ID,
 			)
 			if err != nil {

internal/storage/sqlite/queries.go

@@ -250,6 +250,8 @@ func (s *SQLiteStorage) GetIssue(ctx context.Context, id string) (*types.Issue,
 	var ephemeral sql.NullInt64
 	// Pinned field (bd-7h5)
 	var pinned sql.NullInt64
+	// Template field (beads-1ra)
+	var isTemplate sql.NullInt64
 
 	var contentHash sql.NullString
 	var compactedAtCommit sql.NullString
@@ -259,7 +261,7 @@ func (s *SQLiteStorage) GetIssue(ctx context.Context, id string) (*types.Issue,
 		       created_at, 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
+		       sender, ephemeral, pinned, is_template
 		FROM issues
 		WHERE id = ?
 	`, id).Scan(
@@ -269,7 +271,7 @@ func (s *SQLiteStorage) GetIssue(ctx context.Context, id string) (*types.Issue,
 		&issue.CreatedAt, &issue.UpdatedAt, &closedAt, &externalRef,
 		&issue.CompactionLevel, &compactedAt, &compactedAtCommit, &originalSize, &sourceRepo, &closeReason,
 		&deletedAt, &deletedBy, &deleteReason, &originalType,
-		&sender, &ephemeral, &pinned,
+		&sender, &ephemeral, &pinned, &isTemplate,
 	)
 
 	if err == sql.ErrNoRows {
@@ -331,6 +333,10 @@ func (s *SQLiteStorage) GetIssue(ctx context.Context, id string) (*types.Issue,
 	if pinned.Valid && pinned.Int64 != 0 {
 		issue.Pinned = true
 	}
+	// Template field (beads-1ra)
+	if isTemplate.Valid && isTemplate.Int64 != 0 {
+		issue.IsTemplate = true
+	}
 
 	// Fetch labels for this issue
 	labels, err := s.GetLabels(ctx, issue.ID)
@@ -439,6 +445,8 @@ func (s *SQLiteStorage) GetIssueByExternalRef(ctx context.Context, externalRef s
 	var ephemeral sql.NullInt64
 	// Pinned field (bd-7h5)
 	var pinned sql.NullInt64
+	// Template field (beads-1ra)
+	var isTemplate sql.NullInt64
 
 	err := s.db.QueryRowContext(ctx, `
 		SELECT id, content_hash, title, description, design, acceptance_criteria, notes,
@@ -446,7 +454,7 @@ func (s *SQLiteStorage) GetIssueByExternalRef(ctx context.Context, externalRef s
 		       created_at, 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
+		       sender, ephemeral, pinned, is_template
 		FROM issues
 		WHERE external_ref = ?
 	`, externalRef).Scan(
@@ -456,7 +464,7 @@ func (s *SQLiteStorage) GetIssueByExternalRef(ctx context.Context, externalRef s
 		&issue.CreatedAt, &issue.UpdatedAt, &closedAt, &externalRefCol,
 		&issue.CompactionLevel, &compactedAt, &compactedAtCommit, &originalSize, &sourceRepo, &closeReason,
 		&deletedAt, &deletedBy, &deleteReason, &originalType,
-		&sender, &ephemeral, &pinned,
+		&sender, &ephemeral, &pinned, &isTemplate,
 	)
 
 	if err == sql.ErrNoRows {
@@ -518,6 +526,10 @@ func (s *SQLiteStorage) GetIssueByExternalRef(ctx context.Context, externalRef s
 	if pinned.Valid && pinned.Int64 != 0 {
 		issue.Pinned = true
 	}
+	// Template field (beads-1ra)
+	if isTemplate.Valid && isTemplate.Int64 != 0 {
+		issue.IsTemplate = true
+	}
 
 	// Fetch labels for this issue
 	labels, err := s.GetLabels(ctx, issue.ID)
@@ -1589,6 +1601,15 @@ func (s *SQLiteStorage) SearchIssues(ctx context.Context, query string, filter t
 		}
 	}
 
+	// Template filtering (beads-1ra)
+	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)")
+		}
+	}
+
 	whereSQL := ""
 	if len(whereClauses) > 0 {
 		whereSQL = "WHERE " + strings.Join(whereClauses, " AND ")
@@ -1606,7 +1627,7 @@ func (s *SQLiteStorage) SearchIssues(ctx context.Context, query string, filter t
 		       status, priority, issue_type, assignee, estimated_minutes,
 		       created_at, updated_at, closed_at, external_ref, source_repo, close_reason,
 		       deleted_at, deleted_by, delete_reason, original_type,
-		       sender, ephemeral, pinned
+		       sender, ephemeral, pinned, is_template
 		FROM issues
 		%s
 		ORDER BY priority ASC, created_at DESC

internal/storage/sqlite/ready.go

@@ -110,7 +110,7 @@ func (s *SQLiteStorage) GetReadyWork(ctx context.Context, filter types.WorkFilte
 		i.status, i.priority, i.issue_type, i.assignee, i.estimated_minutes,
 		i.created_at, i.updated_at, i.closed_at, i.external_ref, i.source_repo, i.close_reason,
 		i.deleted_at, i.deleted_by, i.delete_reason, i.original_type,
-		i.sender, i.ephemeral, i.pinned
+		i.sender, i.ephemeral, i.pinned, i.is_template
 		FROM issues i
 		WHERE %s
 		AND NOT EXISTS (
@@ -139,7 +139,7 @@ func (s *SQLiteStorage) GetStaleIssues(ctx context.Context, filter types.StaleFi
 			created_at, updated_at, closed_at, external_ref, source_repo,
 			compaction_level, compacted_at, compacted_at_commit, original_size, close_reason,
 			deleted_at, deleted_by, delete_reason, original_type,
-			sender, ephemeral, pinned
+			sender, ephemeral, pinned, is_template
 		FROM issues
 		WHERE status != 'closed'
 		  AND datetime(updated_at) < datetime('now', '-' || ? || ' days')
@@ -190,6 +190,8 @@ func (s *SQLiteStorage) GetStaleIssues(ctx context.Context, filter types.StaleFi
 		var ephemeral sql.NullInt64
 		// Pinned field (bd-7h5)
 		var pinned sql.NullInt64
+		// Template field (beads-1ra)
+		var isTemplate sql.NullInt64
 
 		err := rows.Scan(
 			&issue.ID, &contentHash, &issue.Title, &issue.Description, &issue.Design,
@@ -198,7 +200,7 @@ func (s *SQLiteStorage) GetStaleIssues(ctx context.Context, filter types.StaleFi
 			&issue.CreatedAt, &issue.UpdatedAt, &closedAt, &externalRef, &sourceRepo,
 			&compactionLevel, &compactedAt, &compactedAtCommit, &originalSize, &closeReason,
 			&deletedAt, &deletedBy, &deleteReason, &originalType,
-			&sender, &ephemeral, &pinned,
+			&sender, &ephemeral, &pinned, &isTemplate,
 		)
 		if err != nil {
 			return nil, fmt.Errorf("failed to scan stale issue: %w", err)
@@ -259,6 +261,10 @@ func (s *SQLiteStorage) GetStaleIssues(ctx context.Context, filter types.StaleFi
 		if pinned.Valid && pinned.Int64 != 0 {
 			issue.Pinned = true
 		}
+		// Template field (beads-1ra)
+		if isTemplate.Valid && isTemplate.Int64 != 0 {
+			issue.IsTemplate = true
+		}
 
 		issues = append(issues, &issue)
 	}

internal/storage/sqlite/schema.go

@@ -32,6 +32,8 @@ CREATE TABLE IF NOT EXISTS issues (
     ephemeral INTEGER DEFAULT 0,
     -- Pinned field (bd-7h5)
     pinned INTEGER DEFAULT 0,
+    -- Template field (beads-1ra)
+    is_template INTEGER DEFAULT 0,
     -- NOTE: replies_to, relates_to, duplicate_of, superseded_by removed per Decision 004
     -- These relationships are now stored in the dependencies table
     CHECK ((status = 'closed') = (closed_at IS NOT NULL))

internal/storage/sqlite/transaction.go

@@ -306,7 +306,7 @@ func (t *sqliteTxStorage) GetIssue(ctx context.Context, id string) (*types.Issue
 		       created_at, 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
+		       sender, ephemeral, pinned, is_template
 		FROM issues
 		WHERE id = ?
 	`, id)
@@ -1107,7 +1107,7 @@ func (t *sqliteTxStorage) SearchIssues(ctx context.Context, query string, filter
 		       created_at, 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
+		       sender, ephemeral, pinned, is_template
 		FROM issues
 		%s
 		ORDER BY priority ASC, created_at DESC
@@ -1152,6 +1152,8 @@ func scanIssueRow(row scanner) (*types.Issue, error) {
 	var ephemeral sql.NullInt64
 	// Pinned field (bd-7h5)
 	var pinned sql.NullInt64
+	// Template field (beads-1ra)
+	var isTemplate sql.NullInt64
 
 	err := row.Scan(
 		&issue.ID, &contentHash, &issue.Title, &issue.Description, &issue.Design,
@@ -1160,7 +1162,7 @@ func scanIssueRow(row scanner) (*types.Issue, error) {
 		&issue.CreatedAt, &issue.UpdatedAt, &closedAt, &externalRef,
 		&issue.CompactionLevel, &compactedAt, &compactedAtCommit, &originalSize, &sourceRepo, &closeReason,
 		&deletedAt, &deletedBy, &deleteReason, &originalType,
-		&sender, &ephemeral, &pinned,
+		&sender, &ephemeral, &pinned, &isTemplate,
 	)
 	if err != nil {
 		return nil, fmt.Errorf("failed to scan issue: %w", err)
@@ -1218,6 +1220,10 @@ func scanIssueRow(row scanner) (*types.Issue, error) {
 	if pinned.Valid && pinned.Int64 != 0 {
 		issue.Pinned = true
 	}
+	// Template field (beads-1ra)
+	if isTemplate.Valid && isTemplate.Int64 != 0 {
+		issue.IsTemplate = true
+	}
 
 	return &issue, nil
 }

internal/types/types.go

@@ -48,6 +48,9 @@ type Issue struct {
 
 	// Pinned field (bd-7h5): persistent context markers
 	Pinned bool `json:"pinned,omitempty"` // If true, issue is a persistent context marker, not a work item
+
+	// Template field (beads-1ra): template molecule support
+	IsTemplate bool `json:"is_template,omitempty"` // If true, issue is a read-only template molecule
 }
 
 // ComputeContentHash creates a deterministic hash of the issue's content.
@@ -83,6 +86,10 @@ func (i *Issue) ComputeContentHash() string {
 	if i.Pinned {
 		h.Write([]byte("pinned"))
 	}
+	h.Write([]byte{0})
+	if i.IsTemplate {
+		h.Write([]byte("template"))
+	}
 
 	return fmt.Sprintf("%x", h.Sum(nil))
 }
@@ -233,7 +240,7 @@ const (
 	TypeChore        IssueType = "chore"
 	TypeMessage      IssueType = "message"       // Ephemeral communication between workers
 	TypeMergeRequest IssueType = "merge-request" // Merge queue entry for refinery processing
-	TypeMolecule     IssueType = "molecule"      // Composable workflow template
+	TypeMolecule     IssueType = "molecule"      // Template molecule for issue hierarchies (beads-1ra)
 )
 
 // IsValid checks if the issue type value is valid
@@ -446,6 +453,9 @@ type IssueFilter struct {
 
 	// Pinned filtering (bd-7h5)
 	Pinned *bool // Filter by pinned flag (nil = any, true = only pinned, false = only non-pinned)
+
+	// Template filtering (beads-1ra)
+	IsTemplate *bool // Filter by template flag (nil = any, true = only templates, false = exclude templates)
 }
 
 // SortPolicy determines how ready work is ordered

internal/utils/path.go

@@ -2,6 +2,7 @@
 package utils
 
 import (
+	"os"
 	"path/filepath"
 )
 
@@ -55,6 +56,19 @@ func FindJSONLInDir(dbDir string) string {
 	return filepath.Join(dbDir, "issues.jsonl")
 }
 
+// FindMoleculesJSONLInDir finds the molecules.jsonl file in the given .beads directory.
+// Returns the path to molecules.jsonl if it exists, empty string otherwise.
+// Molecules are template issues used for instantiation (beads-1ra).
+func FindMoleculesJSONLInDir(dbDir string) string {
+	moleculesPath := filepath.Join(dbDir, "molecules.jsonl")
+	// Check if file exists - we don't fall back to any other file
+	// because molecules.jsonl is optional and specific
+	if _, err := os.Stat(moleculesPath); err == nil {
+		return moleculesPath
+	}
+	return ""
+}
+
 // CanonicalizePath converts a path to its canonical form by:
 // 1. Converting to absolute path
 // 2. Resolving symlinks