Improve minimize_diff target

Mainly more diagnostics.
Add .gitignore in R/
Revert "Sync with transmart/transmartApp-DB"

This reverts commit dfb62d7693e68cfd80a5071f9212c0149b3f865e.
We don't want no duplicated analyses after all.
Separate plugin_module params column into files
Re-apply the RModules analyses changes

Except for the duplication analyses with suffix "pg" and for the
changes to hclust, which look very suspicious.

See https://github.com/transmart/transmartApp-DB/pull/3
Improve vars.sample template
Update README