maker to be run outside of the package dir

Summary of the PR:
- use Makefile outside of a package's directory
- partial rewrite calling shell/R directly instead of using ./maker/include/*R
- removed `increment-version-*`
- added `rd` to generate only `Rd` files using `roxygen` 
- renamed `test` to `tests`

Still to test:
- `clean-vignettes`
- `install-dependencies` , `install-upstream`
- `check-reverse-dependencies`, `check-downstream`

Question:
Shouldn't we want to force install/checking (reverse) deps? It seems that currently, the versions are checked and re-installed only if a more recent version is available.

Added `install-only` and `check-only`.