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This might help...

In the Halo book "Ghosts of Onyx" they discover a "safty world" that was built by the fore runners (as is also implied by the "Arc" in Halo 3)

Based on this and the data terminals found in Halo 3, here's my current understanding:

The forerunners initially tried to fight the flood more conventionally and counld find no means of defeating it.

They then built the Halo project that would destroy all life in the galaxy but...

They also built one (or more) safe havens (Arks) that they could hide in and survivie the cleansing of the Halo rings.