fix: set git index flags on init when sync-branch is configured (#1158)

Fresh clones with sync-branch configured in .beads/config.yaml would show
.beads/issues.jsonl as modified in git status because the git index flags
(skip-worktree, assume-unchanged) are local-only and don't transfer via clone.

This fix ensures bd init sets these flags in two scenarios:
1. `bd init --branch <name>` - when user explicitly sets sync branch
2. `bd init` on cloned repo - when sync-branch already exists in config.yaml

Added SetSyncBranchGitignoreFlags() helper and two tests for coverage.

cmd/bd/init.go

@@ -542,6 +542,23 @@ With --stealth: configures per-repository git settings for invisible beads usage
 			}
 		}
 
+		// Set git index flags to hide JSONL from git status when sync.branch is configured.
+		// These flags are local-only (don't transfer via git clone), so each clone needs them set.
+		// This fixes the issue where fresh clones show .beads/issues.jsonl as modified.
+		if isGitRepo() {
+			if branch != "" {
+				// --branch flag was passed: set flags directly (in-memory config not updated yet)
+				if err := doctor.SetSyncBranchGitignoreFlags(cwd); err != nil && !quiet {
+					fmt.Fprintf(os.Stderr, "Warning: failed to set git index flags: %v\n", err)
+				}
+			} else {
+				// No --branch flag: check if sync-branch exists in config.yaml (cloned repo scenario)
+				if err := doctor.FixSyncBranchGitignore(); err != nil && !quiet {
+					fmt.Fprintf(os.Stderr, "Warning: failed to set git index flags: %v\n", err)
+				}
+			}
+		}
+
 		// Add "landing the plane" instructions to AGENTS.md and @AGENTS.md
 		// Skip in stealth mode (user wants invisible setup) and quiet mode (suppress all output)
 		if !stealth {