Split source files into directories

[onlined]

Description

We added new source files recently and we will in near time. So
for better organization, I split the source files into directories.

Motivation and Context

• Better organization
• Separation of concerns

Checklist

[x] I have not included any built dist files (us maintainers do that prior to a new release)
[] I have added tests covering my changes
[x] All new and existing tests pass
[ ] My changes required the documentation to be updated
  [ ] I have updated the documentation accordingly
  [ ] I have updated the TypeScript 1.8 type definitions accordingly
  [ ] I have updated the TypeScript 2.0+ type definitions accordingly

[arqex]

This PR is a game changer for maintainers. Thanks @onlined !