Docs required

Documentation required settings and flags for pipelines. Now includes the new reference module (e.g. `reference_fasta`) and tries to name namespaces correctly. See #161 (and to a lesser extend #163)

See merge request !174

Force logging to a file

see #158

See merge request !175

Change bwa to bwa-mem

part of #129

See merge request !173

Added executables that are missing on a native osx install

Was installing ide on new mac book and did see some issues in the unit tests

See merge request !171

Fix for issue #167

See merge request !172

NO more reflective issues, simplify some refs.

Remove reflective calls within GearsTrait.

See merge request !170