More involved README restructuring

- Move description of Avro, Parquet, Spark to end, in "Under the Hood" section
- Clarify simple CLI use of `count_kmers`; save more involved scala-code-snippet for `adam-shell` example later on.
- Update some links to non-incubator, yes-apache-project versions.
- De-duplicate blocks showing arg-less `adam-submit` and `adam-submit transform` commands and their full output.
- Move info about installing Spark and setting up ADAM aliases into "Installing" section
- fix relative intra-page links
- update example output of arg-less `adam-submit` and `adam-submit transform` calls
- move "applications" to their own section at the end