fix: hide issues.jsonl from git status when sync.branch configured (GH#870)

When sync.branch is configured, issues.jsonl appears modified in git status
even though changes go to the sync branch. This is confusing for users and
risks accidental commits to the wrong branch.

Implementation:
- Added SyncBranchGitignore() to set git index flags (assume-unchanged,
  skip-worktree) on issues.jsonl when sync.branch is configured
- For untracked files, adds to .git/info/exclude instead
- Called automatically from bd sync after successful sync-branch sync
- Added bd doctor check and fix for this issue
- Added HasSyncBranchGitignoreFlags() to check current flag state
- Added ClearSyncBranchGitignore() to remove flags when sync.branch disabled

Fixes: GH#870 (duplicate of GH#797, GH#801)

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

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

Executed-By: beads/crew/dave
Rig: beads
Role: crew

cmd/bd/doctor/gitignore.go

@@ -7,6 +7,7 @@ import (
 	"path/filepath"
 	"strings"
 
+	"github.com/steveyegge/beads/cmd/bd/doctor/fix"
 	"github.com/steveyegge/beads/internal/syncbranch"
 )
 
@@ -262,3 +263,93 @@ func FixRedirectTracking() error {
 
 	return nil
 }
+
+// CheckSyncBranchGitignore checks if git index flags are set on issues.jsonl when sync.branch is configured.
+// Without these flags, the file appears modified in git status even though changes go to the sync branch.
+// GH#797, GH#801, GH#870.
+func CheckSyncBranchGitignore() DoctorCheck {
+	// Only relevant when sync.branch is configured
+	branch := syncbranch.GetFromYAML()
+	if branch == "" {
+		return DoctorCheck{
+			Name:    "Sync Branch Gitignore",
+			Status:  StatusOK,
+			Message: "N/A (sync.branch not configured)",
+		}
+	}
+
+	issuesPath := filepath.Join(".beads", "issues.jsonl")
+
+	// Check if file exists
+	if _, err := os.Stat(issuesPath); os.IsNotExist(err) {
+		return DoctorCheck{
+			Name:    "Sync Branch Gitignore",
+			Status:  StatusOK,
+			Message: "No issues.jsonl yet",
+		}
+	}
+
+	// Check if file is tracked by git
+	cmd := exec.Command("git", "ls-files", "--error-unmatch", issuesPath) // #nosec G204 - args are hardcoded paths
+	if err := cmd.Run(); err != nil {
+		// File is not tracked - check if it's excluded
+		return DoctorCheck{
+			Name:    "Sync Branch Gitignore",
+			Status:  StatusOK,
+			Message: "issues.jsonl is not tracked (via .gitignore or exclude)",
+		}
+	}
+
+	// File is tracked - check for git index flags
+	cwd, err := os.Getwd()
+	if err != nil {
+		return DoctorCheck{
+			Name:    "Sync Branch Gitignore",
+			Status:  StatusWarning,
+			Message: "Cannot determine current directory",
+		}
+	}
+
+	hasAssumeUnchanged, hasSkipWorktree, err := fix.HasSyncBranchGitignoreFlags(cwd)
+	if err != nil {
+		return DoctorCheck{
+			Name:    "Sync Branch Gitignore",
+			Status:  StatusWarning,
+			Message: "Cannot check git index flags",
+			Detail:  err.Error(),
+		}
+	}
+
+	if hasAssumeUnchanged || hasSkipWorktree {
+		return DoctorCheck{
+			Name:    "Sync Branch Gitignore",
+			Status:  StatusOK,
+			Message: "Git index flags set (issues.jsonl hidden from git status)",
+		}
+	}
+
+	// No flags set - this is the problem case
+	return DoctorCheck{
+		Name:    "Sync Branch Gitignore",
+		Status:  StatusWarning,
+		Message: "issues.jsonl shows as modified (missing git index flags)",
+		Detail:  fmt.Sprintf("sync.branch='%s' configured but issues.jsonl appears in git status", branch),
+		Fix:     "Run 'bd doctor --fix' or 'bd sync' to set git index flags",
+	}
+}
+
+// FixSyncBranchGitignore sets git index flags on issues.jsonl when sync.branch is configured.
+func FixSyncBranchGitignore() error {
+	// Only relevant when sync.branch is configured
+	branch := syncbranch.GetFromYAML()
+	if branch == "" {
+		return nil // Not in sync-branch mode, nothing to do
+	}
+
+	cwd, err := os.Getwd()
+	if err != nil {
+		return fmt.Errorf("cannot determine current directory: %w", err)
+	}
+
+	return fix.SyncBranchGitignore(cwd)
+}