Reorganize source tree

Adjust the source tree layout so that kernel and user space code are
located in seperate directories. We also make these changes:

- Miscellaneous tools (such as `mkfs`) have been moved to `tools`
- All headers (both kernel and user space) are in `include`
- Remove majority of handbook related code
Add hidden swap files to Gitignore
Remove all PAGEBREAK comments
Remove handbook creation targets
Add own README
Adjust copyright
Update README.md

- Adjust header size on "Changes" section
- Adjust Makefile target name for README