Fix flexiprep

Fixing some small issue here found in integration tests.

See merge request !247

Feature fixed values

See #126 

Order of prio of config values:
1. Fixed values
2. User config (-config / -cv on the command line)
3. Default files (coming from BIOPET_CONFIG env)
4. Default values inside the code.

Also changed way to use default values. No need for a merge step anymore, this happens inside the class now. This makes code inside pipelines/extensions cleaner.

Todo:
- [x] Basic implementation
- [x] Unit testing

See merge request !233

Fix errornous foldername

moves folder public/biopet-extentsions -> public/biopet-extensions

See merge request !244

Feature pipeable

Fixes #114 

See merge request !234

Fix for #210

Fixes #210 

See merge request !242

(cherry picked from commit 910074b8)