Damir Vandic b09aee377f 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.

2026-01-19 10:11:16 -08:00

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