Went to actually use the feature in #89 in an Invocations-using project (new Paramiko docs site, as above) and found...I explicitly set it up to merge inner-out, such that a sub-collection wins in conflicts over outer collections. This seems really backwards and I can't tell why I did it that way.
Specifically, I'm distributing Invocations' docs module, which sets defaults for Sphinx project source/build dirs (docs and docs/_build respectively). Then Paramiko's site tries overriding this to be . and _build. That doesn't work because the 'inner' docs module (added to Paramiko's local tasks module as a sub-collection) is winning right now.
Going to reverse the merge order =/
Reverse merge order, fixes #98