coalib: Add coafiles
CliParser: Use right default args for reparse

This was missed during review of 4fd258ac.
settings: Add SectionManager

This adds a Manager object which takes care of all the section stuff,
namely:

- Reading all settings in sections from
    - Default config
    - CLI
    - Configuration file
- Collecting all the bears
- Filling up all needed settings
- Write back the new sections to the configuration file if needed
- Give all information back to caller
SectionManager: Add test
FileCollector: Add from_section constructor
BearRunner: Add control_queue
processes: Add SectionExecutor