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In Illustrator CS5 is there a way to combine all the paths with the same color into the same group?
Yes. Select one of the objects and in the main menu go to Select > Same > Fill Color. Press Ctrl+G on Windows or Cmd+G on Mac to group the selected objects.
Select > Same > Fill Color
In addition to Alexei's answer..
If objects are on the same layer, you can also select the paths and use Pathfinder > Merge. This will combine all shapes with the same color.
Pathfinder > Merge
If the object are touching, the Merge command will combine the objects into one object.
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