Add directory for checkpoint/restart

 - create checkpoints in additional directory within simOutput
 - restart from that directory
 - allow user to set directories application-wide
 - allow to override application-wide settings with HDF5Writer settings
Remove optional cp/rs flags from TBG_macros.cfg
Make --restart-step unset by default and mandatory
Add boost dependencies to INSTALL.md
Merge pull request #376 from f-schmitt-zih/topic-restartDirectories2

Topic restart directories2