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The big problem here is that entities are all very distinct from
each other and can serve very different purposes. Looking at the file
entity, the support for the file entity is very different and needs a
contrib module to support this case. The same is valid for nodes,
comments that are attached to these nodes and users.
Also, the core entity api wasn't flexible enough yet (no criticism)
to support this automatic any-entity indexing case. The dependency
story is only 1 factor in the decision process. As a sitebuilder, you
agree to depend on the modules you choose and also which modules you
install to fit your use case.
It is still based upon assumptions and I agree this might not fit
every use case.
This will probably change in Drupal 8 where entities are really first
Until that time it would be a good idea to start 1 contrib module
for apachesolr that depends on entity_api and allows a generic
indexing method for arbitrary entities and fields. This way the best
of both world would be combined.
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