Now in its third phase, a once decaying row of former factories along Cherry Street and Howard Avenue in the West End is seeing new life. The venture includes the eventual reuse of the former Graphophone Company complex, a rehabilitation that represents a nearly $1 billion investment over six or seven years. The next phase includes a supermarket, additional retail space and more housing. Earlier this year, the state provided a $3.5 million for environmental cleanup in anticipation of the third phase, city officials said. The plan to create a train station and associated development on the East Side between Seaview Avenue and Pembroke Station is essentially dead in the water. The state a few years ago promised funding and then reneged, leaving the $300 million proposal in limbo.