configure_file: canonicalize paths in dependencies

fix duplicate phony edges when configure_file is called on the same file from multiple directories

This addresses the issue outlined here: https://github.com/ninja-build/ninja/pull/1425#issuecomment-435854564

This change affects all generators since the easiest way was to address the issue of .. in paths directly in the configure_file implementation. Also, I've normalized the output as well even though that doesn't seem necessary.

If needed I can revert the output change or even try to make this change affect the ninja generator only.

Fixes: #18584 (closed)
Topic-rename: configure_file-canonical-deps