When I launched Jupyter Notebook application, I saw a whole bunch of files and directories and I realized that it was using my home directory.
After some googling and trial and error, I was able to change the default launch directory that I can keep well organized and that won't clutter my Notebook app!
I ran following line to generate configuration file
$ jupyter notebook --generate-config
Writing default config to: /Users/<your_user>/.jupyter/jupyter_notebook_config.py
After that I was able to edit it to start my Notebook in a directory of my choice.
# The directory to use for notebooks and kernels.
c.NotebookApp.notebook_dir = '/opt/anaconda'
Launched the application through Anaconda Navigator and saw the desired directory used in the start up log
[I 23:49:08.661 NotebookApp] Serving notebooks from local directory: /opt/anaconda
Viola!
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