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The experimental rundir is an attempt to restrict hledger-flow into processing just a subset of files, primarily to quickly get feedback/failures while adding new accounts to an existing set of accounts.
The use case has been described in issue #64.
It is experimental, because the only problem it currently solves is getting hledger-flow to fail fast, and one of the current side effects of doing so is that the generated include files are then written to only include the subset of files that were processed. But as soon as you do a full run again, the include files will be correctly re-generated as before.
Some thought needs to go into properly solving the need for fast failure without causing surprising results. But for now this change should make one of the workarounds currently in use obsolete, namely the use of an old v0.11.1.2 binary which accidentally processed only a subset of files when run in a deeper subdirectory.
If we can arrive at some behaviour that "does the right thing" while only processing a subset of files, then we can consider enabling this by default whenever the basedir is pointed to a deeper subdirectory.