Recompile: fix bundle transport in shallow checkouts#292
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Includes #31346 which replaces git merge --ff-only with a direct ref update when applying bundles, fixing "refusing to merge unrelated histories" and "repository lacks prerequisite commits" errors. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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Picks up gh-aw #31346. Fixes the 'unrelated histories' / 'lacks prerequisite commits' errors blocking all autoloop runs.