maker to be run outside of the package dir

[lgatto]

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.