The British technology firm Autonomy struck millions of dollars’ worth of “handshake deals” through which it paid customers to buy its software, the jury in the fraud trial of its founder, Mike Lynch, has heard.Lynch, who co-founded and led Autonomy, has pleaded not guilty to 16 counts of wire fraud, securities fraud and conspiracy. He stands accused of orchestrating a huge fraud before Hewlett-Packard’s blockbuster takeover of the company in 2011.Since his criminal trial started in San Francisco on Monday, federal prosecutors have alleged Autonomy used a “variety of accounting…