Improve.usage.txt

[sinarueeger]

• I made the README.md and doc/manual.md much slimmer. I mainly removed all the referencepanel part, for which I refer to the usage.txt file. But I did point out the --download.* options.
• added new options to manual.md.
• moved all misc bash and R scripts to a folder called extra/.

Described in issue #85

[aaronmcdaid]

Great work!

I've push a tiny change to this branch to emphasize that, if you need to download the build database again then you should delete the old one. I'm not 100% certain it's necessary, but it can't do any harm!

If you had previous versions of SSIMP installed, you NEED to delete and redownload the database: rm ~/reference_panels/database.of.builds.1kg.uk10k.hrc.2018.01.18.bin ssimp --download.build.db

The download option is equivalant to: # wget https://drive.switch.ch/index.php/s/uOyjAtdvYjxxwZd/download -O ~/reference_panels/database.of.builds.1kg.uk10k.hrc.2018.01.18.bin