Pentagon and lawmakers likely to be at odds over reductions for pet programs.
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Attempt to halt base closure process defeated by wide margin.
Despite negative reaction, Defense officials say employees will ultimately embrace the system.
Pentagon did not wait to follow the National Response Plan, official testifies.
Agency will replace expired contracts using new procurement vehicle.
Squabble over use of continuing contracts stalls negotiations.
Better public, private coordination also needed, panelists say.