Angelina Cando, 30, was arrested in February and charged with arson, criminal mischief and reckless endangerment. All of the charges were categorized as hate crimes.
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Cando appeared briefly in court on Tuesday.
The flag was hanging outside a restaurant in Manhattan. It said "Make America Gay Again" on it.
The incident was caught on camera.
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The fire allegedly set by Cando spread into the building and caused exterior damage. Residents were forced out, but no one was hurt.
The owners of the Little Prince restaurant replaced the flag with another five times its size.
Cando's case is adjourned until May 9 for the Manhattan District Attorney's office to review the findings.
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