Added handling of cache in both cli.py and inference.py

[jimmymcheung]

This is a putative fix to add handling of custom caching directory as intended in the hint of download_fasta_utilities function in fasta_utils.py. See more on issue #13

[jimmymcheung]

Additionally, in commit 51b1e18 I solve a reference problem causing FileNotFoundError when simplefold is called outside of the directory where these python scripts resides. However, from a quick test with protein 7NJS (named in PDB, 445aa), it seems the performance is decreased by ~12%. Validation on this decrease is needed, and potentially further improvements.