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Sorry for being slow to answer questions these days. I've been full steam on a different project.
Two things off the top of my head:
There are flags to control the location of the peru.yaml file, described at the bottom of the Readme. Note that if the two syncs share the same state directory (which they will by default if the destination directory is the same), the second sync will remove the files from the first, so if you want them both to be synced at once you'll need to explicitly specify at least one state directory. (This is perhaps a confusing bit of semantics. We could consider changing it.)
Also, peru has some interesting but rarely-used features for recursive syncing. If you pull in a project that has a peru.yaml of its own, then you can automatically sync the inner project too. This avoids the state issues of the solution above. Any chance your two peru.yaml files are coming from two different repos?
Is it possible to have
peru.yaml
andperu-extra.yaml
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