EAST LYME -- Until three weeks ago, 90 percent of Amy Gully’s daily routine in York Correctional, the state’s only prison for women, was staying in a cell, marking days off a 30-month sentence for embezzlement and waiting her turn to make a phone call home. She told Gov. Dannel P. Malloy that her new routine is dawn-to-dusk activity aimed at preparing her to go home.