I feel your pain.  I also run up against this time and time again and view
it as a significant limitation -- one which often forces me to contort the
structure of my Clojure programs into something less natural.  And as the
Clojure language grows, the problem becomes even more acute.

For example, consider specs.

One common recommendation is to put your specs in a separate, parallel
namespace.

However, implementing specs often requires domain-specific logic, i.e.,
functions from your main namespace.
And your main namespace often requires specs because the logic of your
functions may need the specs in order to conform some data as part of its
processing.

So what to do?  These kinds of things happen a lot in my experience, and a
solution would be incredibly valuable.

Best solution I've found is to hoist mutually dependent things into a
common namespace and use potemkin to clone them into a more logical
partitioning.  But that's never been very satisfactory to me.

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