The idea is group merging:
the user creates a folder for each group of pdf files and places the pdf files belonging to each merging group in a folder named as the final pdf binder. All the pdf files are added into pdfsam that merges them taking care of their belonging group (folder) and saves each final pdf (binder) into its belonging source folder, naming it as its belonging folder. I think this could be done adding three checkboxes:
1. Group (Folder) Merging: the user can set if the files inside different folders will be merged all together (one pdf output file) or will be merged grouping them by folder (many pdf output files as the number of folders).
2. Output: the user can choose to set the output destination folder(s) the same as the input source folder(s).
3. Filenaming: the user says if the output file(s) must be named as the source folder(s) name.

This is very useful when managing grouped files: you wanna merge jobs done by each team member, or your jobs on different subjects, or merge by category, ... but dont want to put them all together.

best regards,