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Fix multi-layer optimization and broken links #7

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We cannot save a proper result_c.csv/plt for multi-layer optimization when we skip --singlelayer because of the following reasons:

  1. Users might not be aware of --num_layer since it isn't listed in the README.md (Basic Usage). Also, the default value of it is 2 which means optimizing the first two layers.
  2. These lines overwrite the existing csv and plt file, so we can only save the last single-layer result.

I address these problems and fix some broken links in the README.md in this pull request.

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