CMakeLists.txt fixes

Part of autoware#23 (closed), copied here for convenience:

Many of the package CMakeLists.txt files in the Autoware.ai stack contain unnecessary and sometimes problematic commands. This was the source of the error in core_planning#11 (closed) and there are many instances of these types of bugs throughout the stack which would not be found until specific environmental changes are made. This issue is to track the clean-up of all CMakeLists.txt files across Autoware.ai.

A script was used to remove unnecessary includes and dependencies, then missing things were manually added to the correct locations if required.