[CMake] Move CMake files into their intended location so the

`contrib/cmake/bootstrap.py` script no longer needs to be executed.

The previous location of the CMake files was a compromise proposed
by @agurfinkel in #461. While this has served us well (allowing progress
to be made) over time limitations of this approach have appeared.

The main problem is that doing many git operations (e.g. pull, rebase)
means the CMake files don't get updated unless the user remembers to
run the script. This can lead to broken and confusing build system
behaviour.

This commit only does the file moving and necessary changes to
`.gitignore`. Other changes will be done in subsequent commits.

.gitignore

@@ -75,14 +75,3 @@ src/api/ml/z3.mllib
 *.bak
 doc/api
 doc/code
-
-# CMake files copied over by the ``contrib/cmake/boostrap.py`` script
-# See #461
-examples/CMakeLists.txt
-examples/*/CMakeLists.txt
-src/CMakeLists.txt
-src/*/CMakeLists.txt
-src/*/*/CMakeLists.txt
-src/*/*/*/CMakeLists.txt
-src/api/dotnet/cmake_install_gac.cmake.in
-src/api/dotnet/cmake_uninstall_gac.cmake.in