Doc step2

[j23414]

Added the step 2 documentation and table of input files:

• https://github.com/isugifNF/polishCLR/blob/doc_step2/docs/Case_01.md#case-1
• https://github.com/isugifNF/polishCLR/blob/doc_step2/docs/Case_02.md#case-2
• https://github.com/isugifNF/polishCLR/blob/doc_step2/docs/Case_03.md#case-3

[Sivanandan]

I will merge this.