Separate operations and checks into steps

[marcospb19]

In a single tree traversal, generate four lists:

1. List of critical issues that require manual intervention.
2. List of warnings.
3. List of intermediate directories to create.
4. List of symlinks to be created.

If any, all items in 1 should be reported together, and the tool should exit.

Otherwise, 2 should be reported.

Then 3 should occur before 4 so that any errors are thrown earlier.

Then 4.

[marcospb19]

This lays the foundation for #3.

[marcospb19]

dotin import is already separated into steps, missing ones now are dotin link and dotin unlink.