Improving recovery mode

[Alteroldis]

Recovery mode needs to be changed. Thus, if an error occurs after all rounds have passed, for example during LTR struct analysis, then the script is not restored at this stage. But the entire workflow is almost done!
v2.0.5
Errors occur due broken dependencies of LTR_retriever or incomplete setting of it paths.

[simone-says]

I'm having this same issue, and when I try to re-run with -recoverDir, it tells me that it looks like a complete RepeatModeler run because all rounds are complete, but LTR_struct hasn't finished.