This also happens with OS Media in hosts_and_hostgroups_helper.rb:

@operatingsystem.media.with_taxonomy_scope_override(@location,@organization)

It looks like changing order of the clauses does help, but it does not look like a proper fix:

[12] pry(main)> SmartProxy.with_features("Puppet CA").with_taxonomy_scope_override(Location.first, Organization.first)
  Location Load (0.2ms)  SELECT "taxonomies".* FROM "taxonomies" WHERE "taxonomies"."type" IN ('Location') ORDER BY title LIMIT 1
  Organization Load (0.1ms)  SELECT "taxonomies".* FROM "taxonomies" WHERE "taxonomies"."type" IN ('Organization') ORDER BY title LIMIT 1
   (0.1ms)  SELECT "taxable_taxonomies"."taxable_id" FROM "taxable_taxonomies" WHERE "taxable_taxonomies"."taxable_type" = 'SmartProxy' AND "taxable_taxonomies"."taxonomy_id" IN (1)
   (0.1ms)  SELECT "taxable_taxonomies"."taxable_id" FROM "taxable_taxonomies" WHERE "taxable_taxonomies"."taxable_type" = 'SmartProxy' AND "taxable_taxonomies"."taxonomy_id" IN (2)
   (0.1ms)  SELECT "taxable_taxonomies"."taxable_id" FROM "taxable_taxonomies" WHERE "taxable_taxonomies"."taxable_type" = 'SmartProxy' AND "taxable_taxonomies"."taxonomy_id" IN (1)
   (0.1ms)  SELECT "taxable_taxonomies"."taxable_id" FROM "taxable_taxonomies" WHERE "taxable_taxonomies"."taxable_type" = 'SmartProxy' AND "taxable_taxonomies"."taxonomy_id" IN (2)
  SmartProxy Load (0.1ms)  SELECT "smart_proxies".* FROM "smart_proxies" WHERE "smart_proxies"."id" IN (2) AND (1=1)
=> [#<SmartProxy id: 2, name: "localhost", url: "http://localhost:8443", created_at: "2013-11-29 12:41:16", updated_at: "2013-11-29 12:41:16">]
[13] pry(main)> 
[14] pry(main)> 
[15] pry(main)> 
[16] pry(main)> SmartProxy.with_taxonomy_scope_override(Location.first, Organization.first).with_features("Puppet CA")
  Location Load (0.2ms)  SELECT "taxonomies".* FROM "taxonomies" WHERE "taxonomies"."type" IN ('Location') ORDER BY title LIMIT 1
  Organization Load (0.1ms)  SELECT "taxonomies".* FROM "taxonomies" WHERE "taxonomies"."type" IN ('Organization') ORDER BY title LIMIT 1
   (0.1ms)  SELECT "taxable_taxonomies"."taxable_id" FROM "taxable_taxonomies" WHERE "taxable_taxonomies"."taxable_type" = 'SmartProxy' AND "taxable_taxonomies"."taxonomy_id" IN (1)
   (0.1ms)  SELECT "taxable_taxonomies"."taxable_id" FROM "taxable_taxonomies" WHERE "taxable_taxonomies"."taxable_type" = 'SmartProxy' AND "taxable_taxonomies"."taxonomy_id" IN (2)
   (0.1ms)  SELECT "taxable_taxonomies"."taxable_id" FROM "taxable_taxonomies" WHERE "taxable_taxonomies"."taxable_type" = 'SmartProxy' AND "taxable_taxonomies"."taxonomy_id" IN (1)
   (0.1ms)  SELECT "taxable_taxonomies"."taxable_id" FROM "taxable_taxonomies" WHERE "taxable_taxonomies"."taxable_type" = 'SmartProxy' AND "taxable_taxonomies"."taxonomy_id" IN (2)
  SmartProxy Load (0.1ms)  SELECT "smart_proxies".* FROM "smart_proxies" INNER JOIN "features_smart_proxies" ON "features_smart_proxies"."smart_proxy_id" = "smart_proxies"."id" INNER JOIN "features" ON "features"."id" = "features_smart_proxies"."feature_id" WHERE "smart_proxies"."id" IN (2) AND "features"."name" IN ('Puppet CA') AND (1=1)
=> []

I think that's an appropriate fix lzap, but it doesn't help with the associations case.

Can't we just change it to

SmartProxy.with_features("Puppet CA").with_taxonomy_scope(@location,@organization) 

which doesn't call .unscoped?

Maybe, it looks like it's giving the right results in a quick check, though I still see it making SQL queries around my Organization.current which is a bit worrying (the idea of the _override method is to ignore the current taxonomy), probably because .with_taxonomy_scope is called from the default_scope still.

I only see SmartProxy.with_taxonomy_scope use the location and organization that were passed in. Another difference between with_taxonomy_scope and with_taxonomy_scope_override scopes is that the former retrieves all children while the latter retrieves all parents of the organization and/or location that were passed in. I think we want the behaviour of SmartProxy.with_taxonomy_scope?

Correction: with_taxonomy_scope will indeed overlap with the default scope if Location.current and Organization.current are set. This doesn't seem to be a problem, however, as when multiple scopes are merged, duplicate attributes are removed, with the last one winning.

A couple of notes/questions:
- We may have bugs where with_taxonomy_scope is applied over the default scope.
- Perhaps it would be better (mostly for clarity/ease of maintenance sake) to explicitly call 'unscoped' in hosts_and_hostgroups_helper.rb (and similar) before using with_taxonomy_scope, ie:

SmartProxy.unscoped.with_features("DNS").with_taxonomy_scope(Location.last, Organization.last)