git apply --3way --check exits 0 even when the real apply would write conflict markers and unmerged index stages, so the previous fix left the worktree dirty on conflicting patches while only flipping changesApplied to false.
Dropped --3way for patch-mode merge and used a --reverse --check probe instead: it succeeds only when the target state is already present (true no-op) and reads without touching the worktree. Conflicts fall through to the normal --check + apply path, which rejects them before writing anything.
Added regression coverage for the conflict scenario asserting the worktree stays clean, and for the fresh apply path.
roboomp
f474fa0e11