Currently `./configure --llvm-root=...` and similar flags will break incremental builds by forcing reconfiguration on every `make`. This happens because `reconfig.mk` incorrectly treats submodules in the `-` (uninitialized) state as requiring reconfiguration, and `./configure` deliberately deinitializes unneeded submodules. The fix is to reconfigure only when submodules are in the `+` state (wrong commit checked out).
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