Package structure reorganisation.

This commit keeps all filenames unchanged, but builds a cleaner
package structure of the IDE.

There are only 5 top-level packages now:
- core
- ui
- logger
- util
- refactoring

Code is split in internal and API packages. Note that this commit
only touches directories, and the API work (clean up, documentation,
interfaces) will follow.

The guideline was to keep related code together. The only exception is
 ui code, that is moved to its top-level package. Additional dimensions
 (for example, following Eclipse concepts like launchers or preferences
 would make it too hard to decide what goes where).

Two unused files were removed:

- JVMUtils
- util/Colors.scala

This organisation makes it easier to see duplicated functionality (like
several RegionOps implicit classes). However, to keep things simple, that work is delayed to follow up PRs, so code changes can be independently 
and easily reviewed.
Moved test files.
Updated package names and imports in sdt.core.
Updated imports/package declarations in tests.
Updated sdt.debug package structure and imports.
Updated debug and debug tests packages.
Updated the spy view.
Updated poms to point to the new location of test suite classes.