Move unrelated functionalities to other packages

[jalew188]

This issue is to make APD cleaner as APD now is doing too much on unrelated stuffs:

• [ ] Move MS data readers to AlphaRaw.
• [ ] Move alphapeptdeep.spec_lib.translate.py to AlphaBase.
• [ ] Move alphapeptdeep.mass_spec to AlphaRaw.
• [ ] Change utils as a folder
• [ ] TODO move alphapeptdeep.rescore to somewhere else.

[jalew188]

Related issues are #93 and #97