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I am doing some integration with a reporting tool and a windows bamboo agent. The working directory on the windows agent is on the C: drive. The installed software I want to integrate with is located on the D: drive. Is there some way I can point the agents sub directory to a different disk on the computer?
Your question appears different from the details you provided. I'm going to try and answer the question and please let me know if I have mis-understood what you are trying to accomplish.
If you are trying to call/execute a *.exe file that is installed on an agent machine have you tried adding it as a "Server capabilities" for local agents, or to the "Capabilities" tab on a remote agent?
From there you should be able to add a "Command" task in your Build Plan or Deployment Project that can call that executable with the parameters that you wish to execute.
I hope that helps answer your question!