Separate Wren VM library sources from CLI tool sources by moving them into
src/vm/ and src/cli/ subdirectories respectively. Update the Makefile to use
separate wildcard patterns for each directory, generate distinct object file
paths under build/vm/ and build/cli/, and adjust include paths to src/include.
Also update the Xcode project file to reference the new file locations.
The guard checks if the VM pointer is NULL or if its methodNames count is zero,
which serves as a heuristic to detect an already-freed VM instance. This prevents
a segmentation fault or memory corruption when wrenFreeVM is called multiple times
on the same VM object.
