Switch basic-run test to work in working directory

Easier to debug
Fix typos in docs
Add ss_mode option to run_ss3model
Add note that change_tv always uses safe mode

Not easy to pass ss_bin argument and no need to use opt version
here anyways.
Add docs in ss3sim_base about ss_mode
Re-document
Merge branch 'feature/ss-renamed' of github.com:ss3sim/ss3sim into feature/ss-renamed

Conflicts:
	tests/basic-run.R