Upper Crust, the gourmet pizza chain that expanded rapidly over the last decade, but in recent years struggled with labor troubles, financial problems, and ownership disputes, has filed for bankruptcy protection. The Boston chain, which defaulted on its loan to TD Bank in late September, said it owes at least $3.4 million, including more than $500,000 to a Brookline construction company, and $229,049 to former Massachusetts attorney general Thomas F. Reilly, who represented the company after leaving office.
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