Fava has an UI to add transactions and code to insert them into the file (which is also used when using Beancount's import system in Fava). The code for it `insert_entry()` lives in
  https://github.com/beancount/fava/blob/master/fava/core/file.py

It works with "custom" directives where one can give a regular expression for the accounts to be inserted in a certain place.

I believe it is against the design of beancount, but is there any existing
code which attempts to add transactions to an existing beancount file.
Assuming the entries in the file are grouped by asset account, it would
need to append the entry to the subsection of entries all from the same
account.

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