Enable the KRuntime to be build in Mono

Changes include:
1. Reorganize the makefile.shade to enable build in Mono. Native projects are skipped.
2. Moving the logic of moving files to it's own batch and bash scripts
3. Update the project.json correspondingly.

Another PR to sake script library is also required to enable build in Mono
https://github.com/sakeproject/sake/pull/15

This has been simply tested in both Mono and Windows. During the PR review, I will test the change extensively.
Ah yeah, the `.mdb` file is only generated when you pass `-debug` to the mcs compiler.