Call manually managed dependencies by that name

Until this change they were called non-bundler dependencies. That made
sense until we started supporting NPM and Pip dependencies.
Remove overly zealous normalization

Having a whole table to store a single boolean seems excessive.
Remove remainder of JRuby specific code and tests

The 'boolean_readers' Sequel plugin handles the differences between the
MRI and JRuby DB adapters.
inline module that is now used in only one place
fix whitespace, caps in CLI help text
remove unused code
make code look a bit more like a table, which it is
remove dead code
remove dead code