Maybe I missed something, but it seemed like beancount wants everything to live in One Giant Journal file. I really wanted a pipeline where each bank statement PDF would output one file with a corresponding list of transactions (this stage can run completely in parallel and I use "ninja" to make it very fast).
Then another process can run over these files looking for matches (+$X, -$X), and spit out "transaction groups", where each transaction group is a set of transaction ids that sum to zero. And then a different interactive tool lets you categorize transactions and spits out transaction groups with embedded "expense" transactions. It's all non-destructive; each tool only adds data, and nothing ever modifies existing files. Then a final step can combine all these files and spit out a beancount file for Fava.
How does this compare with the way beancount's importer does it? How does its importer handle transfers and categorization? Is it destructive or non-destructive?