Make sure a new analysis writes into an empty results folder

[ktrns]

I regularly face the issue that I re-run an analysis, and overwrite old files. Sometimes by mistake. Sometimes on purpose, but then there are often still old files remaining, e.g. because there were more clusters previously.

We should always start with a clean results file.

[ktrns]

Todo:

If the directory is not empty, the script should throw an error; unless overwrite=TRUE ... in that case the results folder is cleared with the exception of the annotation folder; the annotation folder might be taken from a previous analysis on purpose and we need to keep it.