oops, lost genericrepositorytests files in the move... this restores them as
CyderTests...
adds run_dir script
minor changes to output_tools
Merge branch 'develop' into lumped_base_case
output tools merge conflict fix
Merge branch 'develop' into lumped_base_case
Merge branch 'develop' into abstract-db
Merge branch 'abstract-db' into lumped_base_case
lumped case extraction reimplemented