feat(migrate): make orphan branch default for bd migrate sync

[peterkc]

Summary

Make orphan branches the default for bd migrate sync and add --orphan flag for migrating existing branches.

Key behavior:

• New branches: Created as orphan by default (no flag needed)
• Existing branches: Used as-is (backward compatible)
• Migration: Use --orphan to convert existing branch to orphan

Motivation: As suggested in #1125's Alternative section and #1004, orphan branches provide:

• Clean "data sync channel" mental model
• No accidental merge risk (git warns loudly)
• Smaller repository footprint (no stale source code)

Changes

• New sync branches are created as orphan by default
• --orphan flag migrates existing branches (delete + recreate as orphan)
• Safety check prevents data loss when --orphan would delete unpushed commits
• Handles existing worktrees gracefully (removes before branch deletion)
• Uses git commit-tree approach to avoid working directory conflicts
• Existing branches without --orphan are preserved as-is
• Add comprehensive tests for all scenarios
• Add documentation to CLI_REFERENCE.md

Branch Creation Flow

bd migrate sync beads-sync
         |
         v
  ensureDirectMode()
         |
         v
  Branch exists locally/remotely?
        / \
      Yes   No
       |     |
       v     v
  --orphan?  Create orphan (default)
    / \
  Yes   No
   |     |
   v     v
  Has    Use existing
  unpushed?  as-is
    / \
  Yes   No
   |     |
   v     v
  Error  Remove worktree (if exists)
  (or    Delete + recreate orphan
  --force)

Behavior Matrix

Scenario	--orphan	Result
Branch doesn't exist	N/A	Create orphan (default)
Branch exists locally	No	Use as-is (backward compatible)
Branch exists locally	Yes	Migrate: delete + recreate as orphan
Branch exists + unpushed	Yes	Error (use --force to override)
Branch exists + worktree	Yes	Remove worktree first, then migrate
Remote only	No	Fetch from remote
Remote only	Yes	Create local orphan (ignore remote)

Backward Compatibility

Existing users with non-orphan sync branches are NOT affected:

1. branchExistsLocal() detects the existing branch
2. Without --orphan, code uses existing branch as-is
3. Existing sync workflow continues unchanged

To migrate: bd migrate sync <branch> --orphan

Related Issues

• Closes Feature: bd migrate sync --clean to create minimal orphan branch #1125 (Feature: bd migrate sync --clean)
• Implements default orphan behavior from feat: Orphan branch support for sync-branch (cleaner mental model) #1004

Test Plan

• TestMigrateSyncOrphan - Verifies orphan has no merge-base with main
• TestMigrateSyncOrphanWorktree - Verifies worktree works with orphan branches
• TestMigrateSyncExistingBranchPreserved - Verifies existing branches used as-is
• TestMigrateSyncOrphanMigration - Verifies --orphan migrates existing branch
• E2E: Migrated ACF repo from non-orphan to orphan with --orphan --force
• All existing migrate sync tests pass

[peterkc]

CI Note

The lint and version consistency failures are pre-existing issues on main, not caused by this PR.

Lint failures (all in files not touched by this PR):

• cmd/bd/hook.go - errcheck, unparam
• cmd/bd/sync.go - gosec
• internal/storage/dolt/bootstrap.go - gosec

Version mismatch:

• MCP __init__.py has 0.47.2 instead of 0.48.0

This PR only modifies:

• cmd/bd/migrate_sync.go
• cmd/bd/migrate_sync_test.go
• docs/CLI_REFERENCE.md

All tests for migrate_sync pass locally.

[steveyegge]

Merged manually to main with cross-platform fix (replaced /dev/null with --stdin for Windows compatibility). Thanks @peterkc!