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When adding a file to a sketch (using drag and drop, or the Sketch -> Add file... menu item), .o, .a and .so files would be saved into a "code" subdirectory of the sketch. This seems to be a remnant of processing, where also .dll and .jar files could be added to a sketch to be used. In the Arduino IDE, these code files serve no special purpose, and are not treated specially, so it makes no sense to keep this code around. One implication of this is that when "save as" is used, a "code" subdirectory is no longer copied, which might affect people using this "code" subdirectory for other purposes. Similarly, there is support for a "data" subdirectory, in which all other files (that are not sketch source files) are stored, and which is also copied on "save as". Support for this folder is kept intact, since this appears occasionally used (the ESP8266 project uses it to store and upload additional data files, for example). This change was discussed on the mailing list in the "Anyone using "data" and "code" subdirectories in sketches?" thread: https://groups.google.com/a/arduino.cc/forum/#!msg/developers/zPlraPq55ho/ejrLqITnAgAJ