Fix production of low-priority summaries during analysis

After the last changes, low-priority summaries are not produced anymore during analysis. This is due to the PDF files to be merged now being in a wafer subdirectory, which is not taken into account by the in_dir variable, whose assignment was changed in one of the last commits in other parts of the code.

The fix has been tested in a separate dedicated croc_wlt installation, and it has been verified that solves the issue without any (evident) collateral effects.