API doc: update.

Add new Python modules.
Add section on Bash library.
Merge branch 'master' into doc-api
rose namelist-dump: allow (but tidy) zero-padded numeric inputs
Merge pull request #806 from matthewrmshin/doc-api

API doc: update.
Merge pull request #809 from benfitzpatrick/namelist-dump.zero-padded

rose namelist-dump: allow (but tidy) zero-padded numeric inputs