What project is Mary working on in the courtyard?

Mary Reilly is working on a garden in the courtyard. She claims that her master, Dr. Jekyll, gave her permission to do this. Mr. Poole is rather skeptical of Mary's claims as indeed are Dr. Jekyll's housemaids. And besides, Poole is disturbed to see Mary lurking so close to Dr. Jekyll's hidden theater. However, the master of the house himself soon arrives and confirms the truth of what Mary's been saying. We sense a certain degree of mutual understanding and respect between Mary and Dr. Jekyll, one that will develop as the story progresses.
Mary's little garden also provides a metaphor that will come to represent much of the action that follows. She asks Dr. Jekyll why the destructive weeds seem so much stronger than the plants she's trying to nurture. In answer to her own question Mary surmises that it's because the weeds, being wild, have a stronger will to live. In recognizing the truth of this, Mary also implicitly recognizes the truth of what Mr. Hyde represents. He too is a powerful force of nature, just like the destructive weeds.