fix(init): bootstrap from sync-branch when configured (bd-0is)

When sync-branch is configured in config.yaml, bd init now reads from
that branch (origin/<branch> first, then local <branch>) instead of
HEAD. This ensures fresh clones correctly import issues from the sync
branch.

Key changes:
- checkGitForIssues() now returns gitRef (third return value)
- New getLocalSyncBranch() reads sync-branch directly from config.yaml
  (not cached global config) to handle test environments where CWD changes
- importFromGit() accepts gitRef parameter to read from correct branch
- Added readFirstIssueFromGit() for prefix auto-detection from git
- Fixed macOS symlink issue: filepath.EvalSymlinks() ensures /var and
  /private/var paths are normalized before filepath.Rel()

Part of GitHub issue #464 (beads deletes issues in multi-clone environments)

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

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

cmd/bd/autoimport.go

@@ -13,6 +13,7 @@ import (
 	"strings"
 
 	"github.com/steveyegge/beads/internal/storage"
+	"github.com/steveyegge/beads/internal/syncbranch"
 	"github.com/steveyegge/beads/internal/types"
 	"github.com/steveyegge/beads/internal/utils"
 )
@@ -34,7 +35,7 @@ func checkAndAutoImport(ctx context.Context, store storage.Storage) bool {
 	}
 
 	// Database is empty - check if git has issues
-	issueCount, jsonlPath := checkGitForIssues()
+	issueCount, jsonlPath, gitRef := checkGitForIssues()
 	if issueCount == 0 {
 		// No issues in git either
 		return false
@@ -46,7 +47,7 @@ func checkAndAutoImport(ctx context.Context, store storage.Storage) bool {
 	}
 
 	// Import from git
-	if err := importFromGit(ctx, dbPath, store, jsonlPath); err != nil {
+	if err := importFromGit(ctx, dbPath, store, jsonlPath, gitRef); err != nil {
 		if !jsonOutput {
 			fmt.Fprintf(os.Stderr, "Warning: auto-import failed: %v\n", err)
 			fmt.Fprintf(os.Stderr, "Try manually: git show HEAD:%s | bd import -i /dev/stdin\n", jsonlPath)
@@ -61,28 +62,62 @@ func checkAndAutoImport(ctx context.Context, store storage.Storage) bool {
 	return true
 }
 
-// checkGitForIssues checks if git has issues in HEAD:.beads/beads.jsonl or issues.jsonl
-// Returns (issue_count, relative_jsonl_path)
-func checkGitForIssues() (int, string) {
+// checkGitForIssues checks if git has issues in .beads/beads.jsonl or issues.jsonl
+// When sync-branch is configured, reads from that branch; otherwise reads from HEAD.
+// Returns (issue_count, relative_jsonl_path, git_ref)
+func checkGitForIssues() (int, string, string) {
 	// Try to find .beads directory
 	beadsDir := findBeadsDir()
 	if beadsDir == "" {
-		return 0, ""
+		return 0, "", ""
 	}
 
 	// Construct relative path from git root
 	gitRoot := findGitRoot()
 	if gitRoot == "" {
-		return 0, ""
+		return 0, "", ""
 	}
 
+	// Resolve symlinks to ensure consistent paths for filepath.Rel()
+	// This is necessary because on macOS, /var is a symlink to /private/var,
+	// and git rev-parse returns the resolved path while os.Getwd() may not.
+	resolvedBeadsDir, err := filepath.EvalSymlinks(beadsDir)
+	if err != nil {
+		return 0, "", ""
+	}
+	beadsDir = resolvedBeadsDir
+	resolvedGitRoot, err := filepath.EvalSymlinks(gitRoot)
+	if err != nil {
+		return 0, "", ""
+	}
+	gitRoot = resolvedGitRoot
+
 	// Clean paths to ensure consistent separators
 	beadsDir = filepath.Clean(beadsDir)
 	gitRoot = filepath.Clean(gitRoot)
-	
+
 	relBeads, err := filepath.Rel(gitRoot, beadsDir)
 	if err != nil {
-		return 0, ""
+		return 0, "", ""
+	}
+
+	// Determine which branch to read from (bd-0is fix)
+	// If sync-branch is configured in local config.yaml, use it; otherwise fall back to HEAD
+	// We read sync-branch directly from local config file rather than using cached global config
+	// to handle cases where CWD has changed since config initialization (e.g., in tests)
+	gitRef := "HEAD"
+	syncBranch := getLocalSyncBranch(beadsDir)
+	if syncBranch != "" {
+		// Check if the sync branch exists (locally or on remote)
+		// Try origin/<branch> first (more likely to exist in fresh clones),
+		// then local <branch>
+		for _, ref := range []string{"origin/" + syncBranch, syncBranch} {
+			cmd := exec.Command("git", "rev-parse", "--verify", "--quiet", ref) // #nosec G204
+			if err := cmd.Run(); err == nil {
+				gitRef = ref
+				break
+			}
+		}
 	}
 
 	// Try canonical JSONL filenames in precedence order (issues.jsonl is canonical)
@@ -94,17 +129,49 @@ func checkGitForIssues() (int, string) {
 	for _, relPath := range candidates {
 		// Use ToSlash for git path compatibility on Windows
 		gitPath := filepath.ToSlash(relPath)
-		cmd := exec.Command("git", "show", fmt.Sprintf("HEAD:%s", gitPath)) // #nosec G204 - git command with safe args
+		cmd := exec.Command("git", "show", fmt.Sprintf("%s:%s", gitRef, gitPath)) // #nosec G204 - git command with safe args
 		output, err := cmd.Output()
 		if err == nil && len(output) > 0 {
 			lines := bytes.Count(output, []byte("\n"))
 			if lines > 0 {
-				return lines, relPath
+				return lines, relPath, gitRef
 			}
 		}
 	}
 
-	return 0, ""
+	return 0, "", ""
+}
+
+// getLocalSyncBranch reads sync-branch from the local config.yaml file.
+// This reads directly from the file rather than using cached config to handle
+// cases where CWD has changed since config initialization.
+func getLocalSyncBranch(beadsDir string) string {
+	// First check environment variable (highest priority)
+	if envBranch := os.Getenv(syncbranch.EnvVar); envBranch != "" {
+		return envBranch
+	}
+
+	// Read config.yaml directly from the .beads directory
+	configPath := filepath.Join(beadsDir, "config.yaml")
+	data, err := os.ReadFile(configPath) // #nosec G304 - config file path from findBeadsDir
+	if err != nil {
+		return ""
+	}
+
+	// Simple YAML parsing for sync-branch key
+	// Format: "sync-branch: value" or "sync-branch: \"value\""
+	for _, line := range strings.Split(string(data), "\n") {
+		line = strings.TrimSpace(line)
+		if strings.HasPrefix(line, "sync-branch:") {
+			value := strings.TrimPrefix(line, "sync-branch:")
+			value = strings.TrimSpace(value)
+			// Remove quotes if present
+			value = strings.Trim(value, "\"'")
+			return value
+		}
+	}
+
+	return ""
 }
 
 // findBeadsDir finds the .beads directory in current or parent directories
@@ -155,11 +222,11 @@ func findGitRoot() string {
 	return root
 }
 
-// importFromGit imports issues from git HEAD
-func importFromGit(ctx context.Context, dbFilePath string, store storage.Storage, jsonlPath string) error {
+// importFromGit imports issues from git at the specified ref (bd-0is: supports sync-branch)
+func importFromGit(ctx context.Context, dbFilePath string, store storage.Storage, jsonlPath, gitRef string) error {
 	// Get content from git (use ToSlash for Windows compatibility)
 	gitPath := filepath.ToSlash(jsonlPath)
-	cmd := exec.Command("git", "show", fmt.Sprintf("HEAD:%s", gitPath)) // #nosec G204 - git command with safe args
+	cmd := exec.Command("git", "show", fmt.Sprintf("%s:%s", gitRef, gitPath)) // #nosec G204 - git command with safe args
 	jsonlData, err := cmd.Output()
 	if err != nil {
 		return fmt.Errorf("failed to read from git: %w", err)

cmd/bd/autoimport_test.go

@@ -250,13 +250,16 @@ func TestCheckGitForIssues_NoGitRepo(t *testing.T) {
 	tmpDir := t.TempDir()
 	t.Chdir(tmpDir)
 
-	count, path := checkGitForIssues()
+	count, path, gitRef := checkGitForIssues()
 	if count != 0 {
 		t.Errorf("Expected 0 issues, got %d", count)
 	}
 	if path != "" {
 		t.Errorf("Expected empty path, got %s", path)
 	}
+	if gitRef != "" {
+		t.Errorf("Expected empty gitRef, got %s", gitRef)
+	}
 }
 
 func TestCheckGitForIssues_NoBeadsDir(t *testing.T) {
@@ -264,7 +267,7 @@ func TestCheckGitForIssues_NoBeadsDir(t *testing.T) {
 	tmpDir := t.TempDir()
 	t.Chdir(tmpDir)
 
-	count, path := checkGitForIssues()
+	count, path, _ := checkGitForIssues()
 	if count != 0 || path != "" {
 		t.Logf("No .beads dir: count=%d, path=%s (expected 0, empty)", count, path)
 	}

cmd/bd/init.go

@@ -2,6 +2,7 @@ package main
 
 import (
 	"bufio"
+	"bytes"
 	"encoding/json"
 	"fmt"
 	"os"
@@ -89,9 +90,9 @@ With --stealth: configures global git settings for invisible beads usage:
 
 		// auto-detect prefix from first issue in JSONL file
 		if prefix == "" {
-			issueCount, jsonlPath := checkGitForIssues()
+			issueCount, jsonlPath, gitRef := checkGitForIssues()
 			if issueCount > 0 {
-				firstIssue, err := readFirstIssueFromJSONL(jsonlPath)
+				firstIssue, err := readFirstIssueFromGit(jsonlPath, gitRef)
 				if firstIssue != nil && err == nil {
 					prefix = utils.ExtractIssuePrefix(firstIssue.ID)
 				}
@@ -347,16 +348,16 @@ With --stealth: configures global git settings for invisible beads usage:
 		}
 
 		// Check if git has existing issues to import (fresh clone scenario)
-		issueCount, jsonlPath := checkGitForIssues()
+		issueCount, jsonlPath, gitRef := checkGitForIssues()
 		if issueCount > 0 {
 			if !quiet {
 				fmt.Fprintf(os.Stderr, "\n✓ Database initialized. Found %d issues in git, importing...\n", issueCount)
 			}
 
-			if err := importFromGit(ctx, initDBPath, store, jsonlPath); err != nil {
+			if err := importFromGit(ctx, initDBPath, store, jsonlPath, gitRef); err != nil {
 				if !quiet {
 					fmt.Fprintf(os.Stderr, "Warning: auto-import failed: %v\n", err)
-					fmt.Fprintf(os.Stderr, "Try manually: git show HEAD:%s | bd import -i /dev/stdin\n", jsonlPath)
+					fmt.Fprintf(os.Stderr, "Try manually: git show %s:%s | bd import -i /dev/stdin\n", gitRef, jsonlPath)
 				}
 				// Non-fatal - continue with empty database
 			} else if !quiet {
@@ -1208,6 +1209,41 @@ func readFirstIssueFromJSONL(path string) (*types.Issue, error) {
 	return nil, nil
 }
 
+// readFirstIssueFromGit reads the first issue from a git ref (bd-0is: supports sync-branch)
+func readFirstIssueFromGit(jsonlPath, gitRef string) (*types.Issue, error) {
+	// Get content from git (use ToSlash for Windows compatibility)
+	gitPath := filepath.ToSlash(jsonlPath)
+	cmd := exec.Command("git", "show", fmt.Sprintf("%s:%s", gitRef, gitPath)) // #nosec G204
+	output, err := cmd.Output()
+	if err != nil {
+		return nil, fmt.Errorf("failed to read from git: %w", err)
+	}
+
+	scanner := bufio.NewScanner(bytes.NewReader(output))
+	lineNum := 0
+	for scanner.Scan() {
+		lineNum++
+		line := scanner.Text()
+
+		// skip empty lines
+		if line == "" {
+			continue
+		}
+
+		var issue types.Issue
+		if err := json.Unmarshal([]byte(line), &issue); err == nil {
+			return &issue, nil
+		}
+		// Skip malformed lines silently (called during auto-detection)
+	}
+
+	if err := scanner.Err(); err != nil {
+		return nil, fmt.Errorf("error scanning git content: %w", err)
+	}
+
+	return nil, nil
+}
+
 // setupStealthMode configures global git settings for stealth operation
 func setupStealthMode(verbose bool) error {
 	homeDir, err := os.UserHomeDir()

cmd/bd/reinit_test.go

@@ -91,7 +91,7 @@ func testFreshCloneAutoImport(t *testing.T) {
 	// Test checkGitForIssues detects issues.jsonl
 	t.Chdir(dir)
 
-	count, path := checkGitForIssues()
+	count, path, gitRef := checkGitForIssues()
 	if count != 1 {
 		t.Errorf("Expected 1 issue in git, got %d", count)
 	}
@@ -102,7 +102,7 @@ func testFreshCloneAutoImport(t *testing.T) {
 	}
 
 	// Import from git
-	if err := importFromGit(ctx, dbPath, store, path); err != nil {
+	if err := importFromGit(ctx, dbPath, store, path, gitRef); err != nil {
 		t.Fatalf("Import failed: %v", err)
 	}
 
@@ -166,7 +166,7 @@ func testDatabaseRemovalScenario(t *testing.T) {
 	t.Chdir(dir)
 
 	// Test checkGitForIssues finds issues.jsonl (canonical name)
-	count, path := checkGitForIssues()
+	count, path, gitRef := checkGitForIssues()
 	if count != 2 {
 		t.Errorf("Expected 2 issues in git, got %d", count)
 	}
@@ -188,7 +188,7 @@ func testDatabaseRemovalScenario(t *testing.T) {
 		t.Fatalf("Failed to set prefix: %v", err)
 	}
 
-	if err := importFromGit(ctx, dbPath, store, path); err != nil {
+	if err := importFromGit(ctx, dbPath, store, path, gitRef); err != nil {
 		t.Fatalf("Import failed: %v", err)
 	}
 
@@ -244,7 +244,7 @@ func testLegacyFilenameSupport(t *testing.T) {
 	t.Chdir(dir)
 
 	// Test checkGitForIssues finds issues.jsonl
-	count, path := checkGitForIssues()
+	count, path, gitRef := checkGitForIssues()
 	if count != 1 {
 		t.Errorf("Expected 1 issue in git, got %d", count)
 	}
@@ -266,7 +266,7 @@ func testLegacyFilenameSupport(t *testing.T) {
 		t.Fatalf("Failed to set prefix: %v", err)
 	}
 
-	if err := importFromGit(ctx, dbPath, store, path); err != nil {
+	if err := importFromGit(ctx, dbPath, store, path, gitRef); err != nil {
 		t.Fatalf("Import failed: %v", err)
 	}
 
@@ -320,7 +320,7 @@ func testPrecedenceTest(t *testing.T) {
 	t.Chdir(dir)
 
 	// Test checkGitForIssues prefers issues.jsonl
-	count, path := checkGitForIssues()
+	count, path, _ := checkGitForIssues()
 	if count != 2 {
 		t.Errorf("Expected 2 issues (from issues.jsonl), got %d", count)
 	}
@@ -384,7 +384,7 @@ func testInitSafetyCheck(t *testing.T) {
 
 	if stats.TotalIssues == 0 {
 		// Database is empty - check if git has issues
-		recheck, recheckPath := checkGitForIssues()
+		recheck, recheckPath, _ := checkGitForIssues()
 		if recheck == 0 {
 			t.Error("Safety check should have detected issues in git")
 		}