Implement multi-repo hydration layer with mtime caching (bd-307)

- Add repo_mtimes table to track JSONL file modification times
- Implement HydrateFromMultiRepo() with mtime-based skip optimization
- Support tilde expansion for repo paths in config
- Add source_repo column via migration (not in base schema)
- Fix schema to allow migration on existing databases
- Comprehensive test coverage for hydration logic
- Resurrect missing parent issues bd-cb64c226 and bd-cbed9619

Implementation:
- internal/storage/sqlite/multirepo.go - Core hydration logic
- internal/storage/sqlite/multirepo_test.go - Test coverage
- docs/MULTI_REPO_HYDRATION.md - Documentation

Schema changes:
- source_repo column added via migration only (not base schema)
- repo_mtimes table for mtime caching
- All SELECT queries updated to include source_repo

Database recovery:
- Restored from 17 to 285 issues
- Created placeholder parents for orphaned hierarchical children

Amp-Thread-ID: https://ampcode.com/threads/T-faa1339a-14b2-426c-8e18-aa8be6f5cde6
Co-authored-by: Amp <amp@ampcode.com>

internal/storage/sqlite/dependencies.go

@@ -196,7 +196,7 @@ func (s *SQLiteStorage) GetDependenciesWithMetadata(ctx context.Context, issueID
 	rows, err := s.db.QueryContext(ctx, `
 		SELECT i.id, i.content_hash, i.title, i.description, i.design, i.acceptance_criteria, i.notes,
 		       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.created_at, i.updated_at, i.closed_at, i.external_ref, i.source_repo,
 		       d.type
 		FROM issues i
 		JOIN dependencies d ON i.id = d.depends_on_id
@@ -216,7 +216,7 @@ func (s *SQLiteStorage) GetDependentsWithMetadata(ctx context.Context, issueID s
 	rows, err := s.db.QueryContext(ctx, `
 		SELECT i.id, i.content_hash, i.title, i.description, i.design, i.acceptance_criteria, i.notes,
 		       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.created_at, i.updated_at, i.closed_at, i.external_ref, i.source_repo,
 		       d.type
 		FROM issues i
 		JOIN dependencies d ON i.id = d.issue_id
@@ -657,12 +657,13 @@ func (s *SQLiteStorage) scanIssues(ctx context.Context, rows *sql.Rows) ([]*type
 		var estimatedMinutes sql.NullInt64
 		var assignee sql.NullString
 		var externalRef sql.NullString
+		var sourceRepo sql.NullString
 
 		err := rows.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.UpdatedAt, &closedAt, &externalRef,
+			&issue.CreatedAt, &issue.UpdatedAt, &closedAt, &externalRef, &sourceRepo,
 		)
 		if err != nil {
 			return nil, fmt.Errorf("failed to scan issue: %w", err)
@@ -684,6 +685,9 @@ func (s *SQLiteStorage) scanIssues(ctx context.Context, rows *sql.Rows) ([]*type
 		if externalRef.Valid {
 			issue.ExternalRef = &externalRef.String
 		}
+		if sourceRepo.Valid {
+			issue.SourceRepo = sourceRepo.String
+		}
 
 		// Fetch labels for this issue
 		labels, err := s.GetLabels(ctx, issue.ID)
@@ -708,13 +712,14 @@ func (s *SQLiteStorage) scanIssuesWithDependencyType(ctx context.Context, rows *
 		var estimatedMinutes sql.NullInt64
 		var assignee sql.NullString
 		var externalRef sql.NullString
+		var sourceRepo sql.NullString
 		var depType types.DependencyType
 
 		err := rows.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.UpdatedAt, &closedAt, &externalRef,
+			&issue.CreatedAt, &issue.UpdatedAt, &closedAt, &externalRef, &sourceRepo,
 			&depType,
 		)
 		if err != nil {
@@ -737,6 +742,9 @@ func (s *SQLiteStorage) scanIssuesWithDependencyType(ctx context.Context, rows *
 		if externalRef.Valid {
 			issue.ExternalRef = &externalRef.String
 		}
+		if sourceRepo.Valid {
+			issue.SourceRepo = sourceRepo.String
+		}
 
 		// Fetch labels for this issue
 		labels, err := s.GetLabels(ctx, issue.ID)

internal/storage/sqlite/issues.go

@@ -10,18 +10,23 @@ import (
 
 // insertIssue inserts a single issue into the database
 func insertIssue(ctx context.Context, conn *sql.Conn, issue *types.Issue) error {
+	sourceRepo := issue.SourceRepo
+	if sourceRepo == "" {
+		sourceRepo = "." // Default to primary repo
+	}
+	
 	_, err := conn.ExecContext(ctx, `
 		INSERT INTO issues (
 			id, content_hash, title, description, design, acceptance_criteria, notes,
 			status, priority, issue_type, assignee, estimated_minutes,
-			created_at, updated_at, closed_at, external_ref
-		) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
+			created_at, updated_at, closed_at, external_ref, source_repo
+		) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
 	`,
 		issue.ID, issue.ContentHash, issue.Title, issue.Description, issue.Design,
 		issue.AcceptanceCriteria, issue.Notes, issue.Status,
 		issue.Priority, issue.IssueType, issue.Assignee,
 		issue.EstimatedMinutes, issue.CreatedAt, issue.UpdatedAt,
-		issue.ClosedAt, issue.ExternalRef,
+		issue.ClosedAt, issue.ExternalRef, sourceRepo,
 	)
 	if err != nil {
 		return fmt.Errorf("failed to insert issue: %w", err)
@@ -35,8 +40,8 @@ func insertIssues(ctx context.Context, conn *sql.Conn, issues []*types.Issue) er
 		INSERT INTO issues (
 			id, content_hash, title, description, design, acceptance_criteria, notes,
 			status, priority, issue_type, assignee, estimated_minutes,
-			created_at, updated_at, closed_at, external_ref
-		) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
+			created_at, updated_at, closed_at, external_ref, source_repo
+		) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
 	`)
 	if err != nil {
 		return fmt.Errorf("failed to prepare statement: %w", err)
@@ -44,12 +49,17 @@ func insertIssues(ctx context.Context, conn *sql.Conn, issues []*types.Issue) er
 	defer func() { _ = stmt.Close() }()
 
 	for _, issue := range issues {
+		sourceRepo := issue.SourceRepo
+		if sourceRepo == "" {
+			sourceRepo = "." // Default to primary repo
+		}
+		
 		_, err = stmt.ExecContext(ctx,
 			issue.ID, issue.ContentHash, issue.Title, issue.Description, issue.Design,
 			issue.AcceptanceCriteria, issue.Notes, issue.Status,
 			issue.Priority, issue.IssueType, issue.Assignee,
 			issue.EstimatedMinutes, issue.CreatedAt, issue.UpdatedAt,
-			issue.ClosedAt, issue.ExternalRef,
+			issue.ClosedAt, issue.ExternalRef, sourceRepo,
 		)
 		if err != nil {
 			return fmt.Errorf("failed to insert issue %s: %w", issue.ID, err)

internal/storage/sqlite/labels.go

@@ -98,7 +98,7 @@ func (s *SQLiteStorage) GetIssuesByLabel(ctx context.Context, label string) ([]*
 	rows, err := s.db.QueryContext(ctx, `
 		SELECT i.id, i.content_hash, i.title, i.description, i.design, i.acceptance_criteria, i.notes,
 		       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.created_at, i.updated_at, i.closed_at, i.external_ref, i.source_repo
 		FROM issues i
 		JOIN labels l ON i.id = l.issue_id
 		WHERE l.label = ?

internal/storage/sqlite/migrations.go

@@ -29,6 +29,8 @@ var migrations = []Migration{
 	{"export_hashes_table", migrateExportHashesTable},
 	{"content_hash_column", migrateContentHashColumn},
 	{"external_ref_unique", migrateExternalRefUnique},
+	{"source_repo_column", migrateSourceRepoColumn},
+	{"repo_mtimes_table", migrateRepoMtimesTable},
 }
 
 // MigrationInfo contains metadata about a migration for inspection
@@ -64,6 +66,8 @@ func getMigrationDescription(name string) string {
 		"export_hashes_table":          "Adds export_hashes table for idempotent exports",
 		"content_hash_column":          "Adds content_hash column for collision resolution",
 		"external_ref_unique":          "Adds UNIQUE constraint on external_ref column",
+		"source_repo_column":           "Adds source_repo column for multi-repo support",
+		"repo_mtimes_table":            "Adds repo_mtimes table for multi-repo hydration caching",
 	}
 	
 	if desc, ok := descriptions[name]; ok {
@@ -572,3 +576,71 @@ func findExternalRefDuplicates(db *sql.DB) (map[string][]string, error) {
 
 	return duplicates, rows.Err()
 }
+
+// migrateSourceRepoColumn adds source_repo column for multi-repo support (bd-307).
+// Defaults to "." (primary repo) for backward compatibility with existing issues.
+func migrateSourceRepoColumn(db *sql.DB) error {
+	// Check if source_repo column exists
+	var columnExists bool
+	err := db.QueryRow(`
+		SELECT COUNT(*) > 0
+		FROM pragma_table_info('issues')
+		WHERE name = 'source_repo'
+	`).Scan(&columnExists)
+	if err != nil {
+		return fmt.Errorf("failed to check source_repo column: %w", err)
+	}
+
+	if columnExists {
+		// Column already exists
+		return nil
+	}
+
+	// Add source_repo column with default "." (primary repo)
+	_, err = db.Exec(`ALTER TABLE issues ADD COLUMN source_repo TEXT DEFAULT '.'`)
+	if err != nil {
+		return fmt.Errorf("failed to add source_repo column: %w", err)
+	}
+
+	// Create index on source_repo for efficient filtering
+	_, err = db.Exec(`CREATE INDEX IF NOT EXISTS idx_issues_source_repo ON issues(source_repo)`)
+	if err != nil {
+		return fmt.Errorf("failed to create source_repo index: %w", err)
+	}
+
+	return nil
+}
+
+// migrateRepoMtimesTable creates the repo_mtimes table for multi-repo hydration caching (bd-307)
+func migrateRepoMtimesTable(db *sql.DB) error {
+	// Check if repo_mtimes table exists
+	var tableName string
+	err := db.QueryRow(`
+		SELECT name FROM sqlite_master
+		WHERE type='table' AND name='repo_mtimes'
+	`).Scan(&tableName)
+
+	if err == sql.ErrNoRows {
+		// Table doesn't exist, create it
+		_, err := db.Exec(`
+			CREATE TABLE repo_mtimes (
+				repo_path TEXT PRIMARY KEY,
+				jsonl_path TEXT NOT NULL,
+				mtime_ns INTEGER NOT NULL,
+				last_checked DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP
+			);
+			CREATE INDEX idx_repo_mtimes_checked ON repo_mtimes(last_checked);
+		`)
+		if err != nil {
+			return fmt.Errorf("failed to create repo_mtimes table: %w", err)
+		}
+		return nil
+	}
+
+	if err != nil {
+		return fmt.Errorf("failed to check for repo_mtimes table: %w", err)
+	}
+
+	// Table already exists
+	return nil
+}

internal/storage/sqlite/migrations_test.go

@@ -350,6 +350,56 @@ func TestMigrateExternalRefUnique(t *testing.T) {
 	})
 }
 
+func TestMigrateRepoMtimesTable(t *testing.T) {
+	t.Run("creates repo_mtimes table if not exists", func(t *testing.T) {
+		store, cleanup := setupTestDB(t)
+		defer cleanup()
+		db := store.db
+
+		// Drop table if exists
+		_, _ = db.Exec("DROP TABLE IF EXISTS repo_mtimes")
+
+		// Run migration
+		if err := migrateRepoMtimesTable(db); err != nil {
+			t.Fatalf("failed to migrate repo_mtimes table: %v", err)
+		}
+
+		// Verify table exists
+		var tableName string
+		err := db.QueryRow(`
+			SELECT name FROM sqlite_master
+			WHERE type='table' AND name='repo_mtimes'
+		`).Scan(&tableName)
+		if err != nil {
+			t.Fatalf("repo_mtimes table not found: %v", err)
+		}
+	})
+
+	t.Run("is idempotent", func(t *testing.T) {
+		store, cleanup := setupTestDB(t)
+		defer cleanup()
+		db := store.db
+
+		// Run migration twice
+		if err := migrateRepoMtimesTable(db); err != nil {
+			t.Fatalf("first migration failed: %v", err)
+		}
+		if err := migrateRepoMtimesTable(db); err != nil {
+			t.Fatalf("second migration failed: %v", err)
+		}
+
+		// Verify table still exists and is correct
+		var tableName string
+		err := db.QueryRow(`
+			SELECT name FROM sqlite_master
+			WHERE type='table' AND name='repo_mtimes'
+		`).Scan(&tableName)
+		if err != nil {
+			t.Fatalf("repo_mtimes table not found after idempotent migration: %v", err)
+		}
+	})
+}
+
 func TestMigrateContentHashColumn(t *testing.T) {
 	t.Run("adds content_hash column if missing", func(t *testing.T) {
 		s, cleanup := setupTestDB(t)
@@ -426,9 +476,10 @@ func TestMigrateContentHashColumn(t *testing.T) {
 				compacted_at DATETIME,
 				original_size INTEGER,
 				compacted_at_commit TEXT,
+				source_repo 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 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 FROM issues_backup;
 			DROP TABLE issues_backup;
 		`)
 		if err != nil {

internal/storage/sqlite/multirepo.go

@@ -0,0 +1,302 @@
+// Package sqlite implements multi-repo hydration for the SQLite storage backend.
+package sqlite
+
+import (
+	"bufio"
+	"context"
+	"database/sql"
+	"encoding/json"
+	"fmt"
+	"os"
+	"path/filepath"
+	"strings"
+	"time"
+
+	"github.com/steveyegge/beads/internal/config"
+	"github.com/steveyegge/beads/internal/types"
+)
+
+// HydrateFromMultiRepo loads issues from all configured repositories into the database.
+// Uses mtime caching to skip unchanged JSONL files for performance.
+// Returns the number of issues imported from each repo.
+func (s *SQLiteStorage) HydrateFromMultiRepo(ctx context.Context) (map[string]int, error) {
+	// Get multi-repo config
+	multiRepo := config.GetMultiRepoConfig()
+	if multiRepo == nil {
+		// Single-repo mode - nothing to hydrate
+		return nil, nil
+	}
+
+	results := make(map[string]int)
+
+	// Process primary repo first (if set)
+	if multiRepo.Primary != "" {
+		count, err := s.hydrateFromRepo(ctx, multiRepo.Primary, ".")
+		if err != nil {
+			return nil, fmt.Errorf("failed to hydrate primary repo %s: %w", multiRepo.Primary, err)
+		}
+		results["."] = count
+	}
+
+	// Process additional repos
+	for _, repoPath := range multiRepo.Additional {
+		// Expand tilde in path
+		expandedPath, err := expandTilde(repoPath)
+		if err != nil {
+			return nil, fmt.Errorf("failed to expand path %s: %w", repoPath, err)
+		}
+
+		// Use relative path as source_repo identifier
+		relPath := repoPath // Keep original for source_repo field
+		count, err := s.hydrateFromRepo(ctx, expandedPath, relPath)
+		if err != nil {
+			return nil, fmt.Errorf("failed to hydrate repo %s: %w", repoPath, err)
+		}
+		results[relPath] = count
+	}
+
+	return results, nil
+}
+
+// hydrateFromRepo loads issues from a single repository's JSONL file.
+// Uses mtime caching to skip unchanged files.
+func (s *SQLiteStorage) hydrateFromRepo(ctx context.Context, repoPath, sourceRepo string) (int, error) {
+	// Get absolute path to repo
+	absRepoPath, err := filepath.Abs(repoPath)
+	if err != nil {
+		return 0, fmt.Errorf("failed to get absolute path: %w", err)
+	}
+
+	// Construct path to JSONL file
+	jsonlPath := filepath.Join(absRepoPath, ".beads", "issues.jsonl")
+
+	// Check if file exists
+	fileInfo, err := os.Stat(jsonlPath)
+	if err != nil {
+		if os.IsNotExist(err) {
+			// No JSONL file - skip this repo
+			return 0, nil
+		}
+		return 0, fmt.Errorf("failed to stat JSONL file: %w", err)
+	}
+
+	// Get current mtime
+	currentMtime := fileInfo.ModTime().UnixNano()
+
+	// Check cached mtime
+	var cachedMtime int64
+	err = s.db.QueryRowContext(ctx, `
+		SELECT mtime_ns FROM repo_mtimes WHERE repo_path = ?
+	`, absRepoPath).Scan(&cachedMtime)
+
+	if err == nil && cachedMtime == currentMtime {
+		// File hasn't changed - skip import
+		return 0, nil
+	}
+
+	if err != nil && err != sql.ErrNoRows {
+		return 0, fmt.Errorf("failed to query mtime cache: %w", err)
+	}
+
+	// Import issues from JSONL
+	count, err := s.importJSONLFile(ctx, jsonlPath, sourceRepo)
+	if err != nil {
+		return 0, fmt.Errorf("failed to import JSONL: %w", err)
+	}
+
+	// Update mtime cache
+	_, err = s.db.ExecContext(ctx, `
+		INSERT OR REPLACE INTO repo_mtimes (repo_path, jsonl_path, mtime_ns, last_checked)
+		VALUES (?, ?, ?, ?)
+	`, absRepoPath, jsonlPath, currentMtime, time.Now())
+	if err != nil {
+		return 0, fmt.Errorf("failed to update mtime cache: %w", err)
+	}
+
+	return count, nil
+}
+
+// importJSONLFile imports issues from a JSONL file, setting the source_repo field.
+func (s *SQLiteStorage) importJSONLFile(ctx context.Context, jsonlPath, sourceRepo string) (int, error) {
+	file, err := os.Open(jsonlPath)
+	if err != nil {
+		return 0, fmt.Errorf("failed to open JSONL file: %w", err)
+	}
+	defer file.Close()
+
+	scanner := bufio.NewScanner(file)
+	// Increase buffer size for large issues
+	buf := make([]byte, 0, 64*1024)
+	scanner.Buffer(buf, 10*1024*1024) // 10MB max line size
+
+	count := 0
+	lineNum := 0
+
+	// Begin transaction for bulk import
+	tx, err := s.db.BeginTx(ctx, nil)
+	if err != nil {
+		return 0, fmt.Errorf("failed to begin transaction: %w", err)
+	}
+	defer tx.Rollback()
+
+	for scanner.Scan() {
+		lineNum++
+		line := scanner.Text()
+
+		// Skip empty lines and comments
+		if line == "" || strings.HasPrefix(line, "#") {
+			continue
+		}
+
+		var issue types.Issue
+		if err := json.Unmarshal([]byte(line), &issue); err != nil {
+			return 0, fmt.Errorf("failed to parse JSON at line %d: %w", lineNum, err)
+		}
+
+		// Set source_repo field
+		issue.SourceRepo = sourceRepo
+
+		// Compute content hash if missing
+		if issue.ContentHash == "" {
+			issue.ContentHash = issue.ComputeContentHash()
+		}
+
+		// Insert or update issue
+		if err := s.upsertIssueInTx(ctx, tx, &issue); err != nil {
+			return 0, fmt.Errorf("failed to import issue %s at line %d: %w", issue.ID, lineNum, err)
+		}
+
+		count++
+	}
+
+	if err := scanner.Err(); err != nil {
+		return 0, fmt.Errorf("failed to read JSONL file: %w", err)
+	}
+
+	if err := tx.Commit(); err != nil {
+		return 0, fmt.Errorf("failed to commit transaction: %w", err)
+	}
+
+	return count, nil
+}
+
+// upsertIssueInTx inserts or updates an issue within a transaction.
+// Uses INSERT OR REPLACE to handle both new and existing issues.
+func (s *SQLiteStorage) upsertIssueInTx(ctx context.Context, tx *sql.Tx, issue *types.Issue) error {
+	// Validate issue
+	if err := issue.Validate(); err != nil {
+		return fmt.Errorf("validation failed: %w", err)
+	}
+
+	// Check if issue exists
+	var existingID string
+	err := tx.QueryRowContext(ctx, `SELECT id FROM issues WHERE id = ?`, issue.ID).Scan(&existingID)
+	
+	if err == sql.ErrNoRows {
+		// Issue doesn't exist - insert it
+		_, 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, updated_at, closed_at, external_ref, source_repo
+			) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
+		`,
+			issue.ID, issue.ContentHash, issue.Title, issue.Description, issue.Design,
+			issue.AcceptanceCriteria, issue.Notes, issue.Status,
+			issue.Priority, issue.IssueType, issue.Assignee,
+			issue.EstimatedMinutes, issue.CreatedAt, issue.UpdatedAt,
+			issue.ClosedAt, issue.ExternalRef, issue.SourceRepo,
+		)
+		if err != nil {
+			return fmt.Errorf("failed to insert issue: %w", err)
+		}
+	} else if err != nil {
+		return fmt.Errorf("failed to check existing issue: %w", err)
+	} else {
+		// Issue exists - update it
+		// Only update if content_hash is different (avoid unnecessary writes)
+		var existingHash string
+		err = tx.QueryRowContext(ctx, `SELECT content_hash FROM issues WHERE id = ?`, issue.ID).Scan(&existingHash)
+		if err != nil {
+			return fmt.Errorf("failed to get existing hash: %w", err)
+		}
+
+		if existingHash != issue.ContentHash {
+			_, err = tx.ExecContext(ctx, `
+				UPDATE issues SET
+					content_hash = ?, title = ?, description = ?, design = ?,
+					acceptance_criteria = ?, notes = ?, status = ?, priority = ?,
+					issue_type = ?, assignee = ?, estimated_minutes = ?,
+					updated_at = ?, closed_at = ?, external_ref = ?, source_repo = ?
+				WHERE id = ?
+			`,
+				issue.ContentHash, issue.Title, issue.Description, issue.Design,
+				issue.AcceptanceCriteria, issue.Notes, issue.Status, issue.Priority,
+				issue.IssueType, issue.Assignee, issue.EstimatedMinutes,
+				issue.UpdatedAt, issue.ClosedAt, issue.ExternalRef, issue.SourceRepo,
+				issue.ID,
+			)
+			if err != nil {
+				return fmt.Errorf("failed to update issue: %w", err)
+			}
+		}
+	}
+
+	// Import dependencies if present
+	for _, dep := range issue.Dependencies {
+		_, err = tx.ExecContext(ctx, `
+			INSERT OR IGNORE INTO dependencies (issue_id, depends_on_id, type, created_at, created_by)
+			VALUES (?, ?, ?, ?, ?)
+		`, dep.IssueID, dep.DependsOnID, dep.Type, dep.CreatedAt, dep.CreatedBy)
+		if err != nil {
+			return fmt.Errorf("failed to import dependency: %w", err)
+		}
+	}
+
+	// Import labels if present
+	for _, label := range issue.Labels {
+		_, err = tx.ExecContext(ctx, `
+			INSERT OR IGNORE INTO labels (issue_id, label)
+			VALUES (?, ?)
+		`, issue.ID, label)
+		if err != nil {
+			return fmt.Errorf("failed to import label: %w", err)
+		}
+	}
+
+	// Import comments if present
+	for _, comment := range issue.Comments {
+		_, err = tx.ExecContext(ctx, `
+			INSERT OR IGNORE INTO comments (id, issue_id, author, text, created_at)
+			VALUES (?, ?, ?, ?, ?)
+		`, comment.ID, comment.IssueID, comment.Author, comment.Text, comment.CreatedAt)
+		if err != nil {
+			return fmt.Errorf("failed to import comment: %w", err)
+		}
+	}
+
+	return nil
+}
+
+// expandTilde expands ~ in a file path to the user's home directory.
+func expandTilde(path string) (string, error) {
+	if !strings.HasPrefix(path, "~") {
+		return path, nil
+	}
+
+	homeDir, err := os.UserHomeDir()
+	if err != nil {
+		return "", fmt.Errorf("failed to get home directory: %w", err)
+	}
+
+	if path == "~" {
+		return homeDir, nil
+	}
+
+	if strings.HasPrefix(path, "~/") {
+		return filepath.Join(homeDir, path[2:]), nil
+	}
+
+	// ~user not supported
+	return path, nil
+}

internal/storage/sqlite/multirepo_test.go

@@ -0,0 +1,375 @@
+package sqlite
+
+import (
+	"context"
+	"encoding/json"
+	"os"
+	"path/filepath"
+	"testing"
+	"time"
+
+	"github.com/steveyegge/beads/internal/config"
+	"github.com/steveyegge/beads/internal/types"
+)
+
+func TestExpandTilde(t *testing.T) {
+	tests := []struct {
+		name    string
+		path    string
+		wantErr bool
+	}{
+		{"no tilde", "/absolute/path", false},
+		{"tilde alone", "~", false},
+		{"tilde with path", "~/Documents", false},
+		{"relative path", "relative/path", false},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			result, err := expandTilde(tt.path)
+			if (err != nil) != tt.wantErr {
+				t.Errorf("expandTilde() error = %v, wantErr %v", err, tt.wantErr)
+				return
+			}
+			if !tt.wantErr && result == "" {
+				t.Error("expandTilde() returned empty string")
+			}
+		})
+	}
+}
+
+func TestHydrateFromMultiRepo(t *testing.T) {
+	t.Run("single-repo mode returns nil", func(t *testing.T) {
+		store, cleanup := setupTestDB(t)
+		defer cleanup()
+
+		// No multi-repo config - should return nil
+		ctx := context.Background()
+		results, err := store.HydrateFromMultiRepo(ctx)
+		if err != nil {
+			t.Fatalf("HydrateFromMultiRepo() error = %v", err)
+		}
+		if results != nil {
+			t.Errorf("expected nil results in single-repo mode, got %v", results)
+		}
+	})
+
+	t.Run("hydrates from primary repo", func(t *testing.T) {
+		store, cleanup := setupTestDB(t)
+		defer cleanup()
+
+		// Initialize config
+		if err := config.Initialize(); err != nil {
+			t.Fatalf("failed to initialize config: %v", err)
+		}
+
+		// Create temporary repo with JSONL file
+		tmpDir := t.TempDir()
+		beadsDir := filepath.Join(tmpDir, ".beads")
+		if err := os.MkdirAll(beadsDir, 0755); err != nil {
+			t.Fatalf("failed to create .beads dir: %v", err)
+		}
+
+		// Create test issue
+		issue := types.Issue{
+			ID:          "test-1",
+			Title:       "Test Issue",
+			Status:      types.StatusOpen,
+			Priority:    1,
+			IssueType:   types.TypeTask,
+			CreatedAt:   time.Now(),
+			UpdatedAt:   time.Now(),
+			SourceRepo:  ".",
+		}
+		issue.ContentHash = issue.ComputeContentHash()
+
+		// Write JSONL file
+		jsonlPath := filepath.Join(beadsDir, "issues.jsonl")
+		f, err := os.Create(jsonlPath)
+		if err != nil {
+			t.Fatalf("failed to create JSONL file: %v", err)
+		}
+		enc := json.NewEncoder(f)
+		if err := enc.Encode(issue); err != nil {
+			f.Close()
+			t.Fatalf("failed to write issue: %v", err)
+		}
+		f.Close()
+
+		// Set multi-repo config
+		config.Set("repos.primary", tmpDir)
+
+		ctx := context.Background()
+		results, err := store.HydrateFromMultiRepo(ctx)
+		if err != nil {
+			t.Fatalf("HydrateFromMultiRepo() error = %v", err)
+		}
+
+		if results == nil || results["."] != 1 {
+			t.Errorf("expected 1 issue from primary repo, got %v", results)
+		}
+
+		// Verify issue was imported
+		imported, err := store.GetIssue(ctx, "test-1")
+		if err != nil {
+			t.Fatalf("failed to get imported issue: %v", err)
+		}
+		if imported.Title != "Test Issue" {
+			t.Errorf("expected title 'Test Issue', got %q", imported.Title)
+		}
+		if imported.SourceRepo != "." {
+			t.Errorf("expected source_repo '.', got %q", imported.SourceRepo)
+		}
+
+		// Clean up config
+		config.Set("repos.primary", "")
+	})
+
+	t.Run("uses mtime caching to skip unchanged files", func(t *testing.T) {
+		store, cleanup := setupTestDB(t)
+		defer cleanup()
+
+		// Initialize config
+		if err := config.Initialize(); err != nil {
+			t.Fatalf("failed to initialize config: %v", err)
+		}
+
+		// Create temporary repo with JSONL file
+		tmpDir := t.TempDir()
+		beadsDir := filepath.Join(tmpDir, ".beads")
+		if err := os.MkdirAll(beadsDir, 0755); err != nil {
+			t.Fatalf("failed to create .beads dir: %v", err)
+		}
+
+		// Create test issue
+		issue := types.Issue{
+			ID:          "test-2",
+			Title:       "Test Issue 2",
+			Status:      types.StatusOpen,
+			Priority:    1,
+			IssueType:   types.TypeTask,
+			CreatedAt:   time.Now(),
+			UpdatedAt:   time.Now(),
+			SourceRepo:  ".",
+		}
+		issue.ContentHash = issue.ComputeContentHash()
+
+		// Write JSONL file
+		jsonlPath := filepath.Join(beadsDir, "issues.jsonl")
+		f, err := os.Create(jsonlPath)
+		if err != nil {
+			t.Fatalf("failed to create JSONL file: %v", err)
+		}
+		enc := json.NewEncoder(f)
+		if err := enc.Encode(issue); err != nil {
+			f.Close()
+			t.Fatalf("failed to write issue: %v", err)
+		}
+		f.Close()
+
+		// Set multi-repo config
+		config.Set("repos.primary", tmpDir)
+
+		ctx := context.Background()
+
+		// First hydration - should import
+		results1, err := store.HydrateFromMultiRepo(ctx)
+		if err != nil {
+			t.Fatalf("first HydrateFromMultiRepo() error = %v", err)
+		}
+		if results1["."] != 1 {
+			t.Errorf("first hydration: expected 1 issue, got %d", results1["."])
+		}
+
+		// Second hydration - should skip (mtime unchanged)
+		results2, err := store.HydrateFromMultiRepo(ctx)
+		if err != nil {
+			t.Fatalf("second HydrateFromMultiRepo() error = %v", err)
+		}
+		if results2["."] != 0 {
+			t.Errorf("second hydration: expected 0 issues (cached), got %d", results2["."])
+		}
+	})
+
+	t.Run("imports additional repos", func(t *testing.T) {
+		store, cleanup := setupTestDB(t)
+		defer cleanup()
+
+		// Initialize config
+		if err := config.Initialize(); err != nil {
+			t.Fatalf("failed to initialize config: %v", err)
+		}
+
+		// Create primary repo
+		primaryDir := t.TempDir()
+		primaryBeadsDir := filepath.Join(primaryDir, ".beads")
+		if err := os.MkdirAll(primaryBeadsDir, 0755); err != nil {
+			t.Fatalf("failed to create primary .beads dir: %v", err)
+		}
+
+		issue1 := types.Issue{
+			ID:         "primary-1",
+			Title:      "Primary Issue",
+			Status:     types.StatusOpen,
+			Priority:   1,
+			IssueType:  types.TypeTask,
+			CreatedAt:  time.Now(),
+			UpdatedAt:  time.Now(),
+			SourceRepo: ".",
+		}
+		issue1.ContentHash = issue1.ComputeContentHash()
+
+		f1, err := os.Create(filepath.Join(primaryBeadsDir, "issues.jsonl"))
+		if err != nil {
+			t.Fatalf("failed to create primary JSONL: %v", err)
+		}
+		json.NewEncoder(f1).Encode(issue1)
+		f1.Close()
+
+		// Create additional repo
+		additionalDir := t.TempDir()
+		additionalBeadsDir := filepath.Join(additionalDir, ".beads")
+		if err := os.MkdirAll(additionalBeadsDir, 0755); err != nil {
+			t.Fatalf("failed to create additional .beads dir: %v", err)
+		}
+
+		issue2 := types.Issue{
+			ID:         "additional-1",
+			Title:      "Additional Issue",
+			Status:     types.StatusOpen,
+			Priority:   1,
+			IssueType:  types.TypeTask,
+			CreatedAt:  time.Now(),
+			UpdatedAt:  time.Now(),
+			SourceRepo: additionalDir,
+		}
+		issue2.ContentHash = issue2.ComputeContentHash()
+
+		f2, err := os.Create(filepath.Join(additionalBeadsDir, "issues.jsonl"))
+		if err != nil {
+			t.Fatalf("failed to create additional JSONL: %v", err)
+		}
+		json.NewEncoder(f2).Encode(issue2)
+		f2.Close()
+
+		// Set multi-repo config
+		config.Set("repos.primary", primaryDir)
+		config.Set("repos.additional", []string{additionalDir})
+
+		ctx := context.Background()
+		results, err := store.HydrateFromMultiRepo(ctx)
+		if err != nil {
+			t.Fatalf("HydrateFromMultiRepo() error = %v", err)
+		}
+
+		if results["."] != 1 {
+			t.Errorf("expected 1 issue from primary, got %d", results["."])
+		}
+		if results[additionalDir] != 1 {
+			t.Errorf("expected 1 issue from additional, got %d", results[additionalDir])
+		}
+
+		// Verify both issues were imported
+		primary, err := store.GetIssue(ctx, "primary-1")
+		if err != nil {
+			t.Fatalf("failed to get primary issue: %v", err)
+		}
+		if primary.SourceRepo != "." {
+			t.Errorf("primary issue: expected source_repo '.', got %q", primary.SourceRepo)
+		}
+
+		additional, err := store.GetIssue(ctx, "additional-1")
+		if err != nil {
+			t.Fatalf("failed to get additional issue: %v", err)
+		}
+		if additional.SourceRepo != additionalDir {
+			t.Errorf("additional issue: expected source_repo %q, got %q", additionalDir, additional.SourceRepo)
+		}
+	})
+}
+
+func TestImportJSONLFile(t *testing.T) {
+	t.Run("imports issues with dependencies and labels", func(t *testing.T) {
+		store, cleanup := setupTestDB(t)
+		defer cleanup()
+
+		// Create test JSONL file
+		tmpDir := t.TempDir()
+		jsonlPath := filepath.Join(tmpDir, "test.jsonl")
+		f, err := os.Create(jsonlPath)
+		if err != nil {
+			t.Fatalf("failed to create JSONL file: %v", err)
+		}
+
+		// Create issues with dependencies and labels
+		issue1 := types.Issue{
+			ID:         "test-1",
+			Title:      "Issue 1",
+			Status:     types.StatusOpen,
+			Priority:   1,
+			IssueType:  types.TypeTask,
+			CreatedAt:  time.Now(),
+			UpdatedAt:  time.Now(),
+			Labels:     []string{"bug", "critical"},
+			SourceRepo: "test",
+		}
+		issue1.ContentHash = issue1.ComputeContentHash()
+
+		issue2 := types.Issue{
+			ID:        "test-2",
+			Title:     "Issue 2",
+			Status:    types.StatusOpen,
+			Priority:  2,
+			IssueType: types.TypeTask,
+			CreatedAt: time.Now(),
+			UpdatedAt: time.Now(),
+			Dependencies: []*types.Dependency{
+				{
+					IssueID:     "test-2",
+					DependsOnID: "test-1",
+					Type:        types.DepBlocks,
+					CreatedAt:   time.Now(),
+					CreatedBy:   "test",
+				},
+			},
+			SourceRepo: "test",
+		}
+		issue2.ContentHash = issue2.ComputeContentHash()
+
+		enc := json.NewEncoder(f)
+		enc.Encode(issue1)
+		enc.Encode(issue2)
+		f.Close()
+
+		// Import
+		ctx := context.Background()
+		count, err := store.importJSONLFile(ctx, jsonlPath, "test")
+		if err != nil {
+			t.Fatalf("importJSONLFile() error = %v", err)
+		}
+		if count != 2 {
+			t.Errorf("expected 2 issues imported, got %d", count)
+		}
+
+		// Verify issues
+		imported1, err := store.GetIssue(ctx, "test-1")
+		if err != nil {
+			t.Fatalf("failed to get issue 1: %v", err)
+		}
+		if len(imported1.Labels) != 2 {
+			t.Errorf("expected 2 labels, got %d", len(imported1.Labels))
+		}
+
+		// Verify dependency
+		deps, err := store.GetDependencies(ctx, "test-2")
+		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 len(deps) > 0 && deps[0].ID != "test-1" {
+			t.Errorf("expected dependency on test-1, got %s", deps[0].ID)
+		}
+	})
+}

internal/storage/sqlite/ready.go

@@ -117,7 +117,7 @@ func (s *SQLiteStorage) GetReadyWork(ctx context.Context, filter types.WorkFilte
 		-- Step 3: Select ready issues (excluding all blocked)
 		SELECT i.id, i.content_hash, i.title, i.description, i.design, i.acceptance_criteria, i.notes,
 		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.created_at, i.updated_at, i.closed_at, i.external_ref, i.source_repo
 		FROM issues i
 		WHERE %s
 		AND NOT EXISTS (
@@ -143,7 +143,7 @@ func (s *SQLiteStorage) GetStaleIssues(ctx context.Context, filter types.StaleFi
 		SELECT
 			id, content_hash, title, description, design, acceptance_criteria, notes,
 			status, priority, issue_type, assignee, estimated_minutes,
-			created_at, updated_at, closed_at, external_ref,
+			created_at, updated_at, closed_at, external_ref, source_repo,
 			compaction_level, compacted_at, compacted_at_commit, original_size
 		FROM issues
 		WHERE status != 'closed'
@@ -238,7 +238,7 @@ func (s *SQLiteStorage) GetBlockedIssues(ctx context.Context) ([]*types.BlockedI
 		SELECT
 		    i.id, i.title, i.description, i.design, i.acceptance_criteria, i.notes,
 		    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.created_at, i.updated_at, i.closed_at, i.external_ref, i.source_repo,
 		    COUNT(d.depends_on_id) as blocked_by_count,
 		    GROUP_CONCAT(d.depends_on_id, ',') as blocker_ids
 		FROM issues i
@@ -262,13 +262,14 @@ func (s *SQLiteStorage) GetBlockedIssues(ctx context.Context) ([]*types.BlockedI
 		var estimatedMinutes sql.NullInt64
 		var assignee sql.NullString
 		var externalRef sql.NullString
+		var sourceRepo sql.NullString
 		var blockerIDsStr string
 
 		err := rows.Scan(
 			&issue.ID, &issue.Title, &issue.Description, &issue.Design,
 			&issue.AcceptanceCriteria, &issue.Notes, &issue.Status,
 			&issue.Priority, &issue.IssueType, &assignee, &estimatedMinutes,
-			&issue.CreatedAt, &issue.UpdatedAt, &closedAt, &externalRef, &issue.BlockedByCount,
+			&issue.CreatedAt, &issue.UpdatedAt, &closedAt, &externalRef, &sourceRepo, &issue.BlockedByCount,
 			&blockerIDsStr,
 		)
 		if err != nil {
@@ -288,6 +289,9 @@ func (s *SQLiteStorage) GetBlockedIssues(ctx context.Context) ([]*types.BlockedI
 		if externalRef.Valid {
 			issue.ExternalRef = &externalRef.String
 		}
+		if sourceRepo.Valid {
+			issue.SourceRepo = sourceRepo.String
+		}
 
 		// Parse comma-separated blocker IDs
 		if blockerIDsStr != "" {

internal/storage/sqlite/schema.go

@@ -166,6 +166,17 @@ CREATE TABLE IF NOT EXISTS compaction_snapshots (
 
 CREATE INDEX IF NOT EXISTS idx_comp_snap_issue_level_created ON compaction_snapshots(issue_id, compaction_level, created_at DESC);
 
+-- Repository mtimes table (for multi-repo hydration optimization)
+-- Tracks modification times of JSONL files to skip unchanged repos
+CREATE TABLE IF NOT EXISTS repo_mtimes (
+    repo_path TEXT PRIMARY KEY,  -- Absolute path to the repository root
+    jsonl_path TEXT NOT NULL,    -- Absolute path to the .beads/issues.jsonl file
+    mtime_ns INTEGER NOT NULL,   -- Modification time in nanoseconds since epoch
+    last_checked DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP
+);
+
+CREATE INDEX IF NOT EXISTS idx_repo_mtimes_checked ON repo_mtimes(last_checked);
+
 -- Ready work view (with hierarchical blocking)
 -- Uses recursive CTE to propagate blocking through parent-child hierarchy
 CREATE VIEW IF NOT EXISTS ready_issues AS

internal/storage/sqlite/sqlite.go

@@ -88,10 +88,22 @@ func New(path string) (*SQLiteStorage, error) {
 		}
 	}
 
-	return &SQLiteStorage{
+	storage := &SQLiteStorage{
 		db:     db,
 		dbPath: absPath,
-	}, nil
+	}
+
+	// Hydrate from multi-repo config if configured (bd-307)
+	// Skip for in-memory databases (used in tests)
+	if path != ":memory:" {
+		ctx := context.Background()
+		_, err := storage.HydrateFromMultiRepo(ctx)
+		if err != nil {
+			return nil, fmt.Errorf("failed to hydrate from multi-repo: %w", err)
+		}
+	}
+
+	return storage, nil
 }
 
 // REMOVED (bd-8e05): getNextIDForPrefix and AllocateNextID - sequential ID generation
@@ -231,6 +243,7 @@ func (s *SQLiteStorage) GetIssue(ctx context.Context, id string) (*types.Issue,
 	var externalRef sql.NullString
 	var compactedAt sql.NullTime
 	var originalSize sql.NullInt64
+	var sourceRepo sql.NullString
 
 	var contentHash sql.NullString
 	var compactedAtCommit sql.NullString
@@ -238,7 +251,7 @@ func (s *SQLiteStorage) GetIssue(ctx context.Context, id string) (*types.Issue,
 		SELECT id, content_hash, 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, compacted_at_commit, original_size
+		       compaction_level, compacted_at, compacted_at_commit, original_size, source_repo
 		FROM issues
 		WHERE id = ?
 	`, id).Scan(
@@ -246,7 +259,7 @@ func (s *SQLiteStorage) GetIssue(ctx context.Context, id string) (*types.Issue,
 		&issue.AcceptanceCriteria, &issue.Notes, &issue.Status,
 		&issue.Priority, &issue.IssueType, &assignee, &estimatedMinutes,
 		&issue.CreatedAt, &issue.UpdatedAt, &closedAt, &externalRef,
-		&issue.CompactionLevel, &compactedAt, &compactedAtCommit, &originalSize,
+		&issue.CompactionLevel, &compactedAt, &compactedAtCommit, &originalSize, &sourceRepo,
 	)
 
 	if err == sql.ErrNoRows {
@@ -281,6 +294,9 @@ func (s *SQLiteStorage) GetIssue(ctx context.Context, id string) (*types.Issue,
 	if originalSize.Valid {
 		issue.OriginalSize = int(originalSize.Int64)
 	}
+	if sourceRepo.Valid {
+		issue.SourceRepo = sourceRepo.String
+	}
 
 	// Fetch labels for this issue
 	labels, err := s.GetLabels(ctx, issue.ID)
@@ -1132,7 +1148,7 @@ func (s *SQLiteStorage) SearchIssues(ctx context.Context, query string, filter t
 	querySQL := fmt.Sprintf(`
 		SELECT id, content_hash, title, description, design, acceptance_criteria, notes,
 		       status, priority, issue_type, assignee, estimated_minutes,
-		       created_at, updated_at, closed_at, external_ref
+		       created_at, updated_at, closed_at, external_ref, source_repo
 		FROM issues
 		%s
 		ORDER BY priority ASC, created_at DESC