Replacing directory with a regular file breaks squashing

[Nixxx11]

FROM busybox:1.36.1
RUN mkdir /tmp/dir
RUN touch /tmp/dir/file
RUN rm -rf /tmp/dir ; touch /tmp/dir

Squashing this image will produce a broken image containing both /tmp/dir/file and /tmp/dir (second one is a regular file, not a directory). This problem was solved earlier for symlinks (#120 ?), but it is exactly the same for all other types of files

And here is a similar scenario for marker files:

FROM busybox:1.36.1
RUN mkdir /tmp/dir
RUN touch /tmp/dir/file
RUN rm /tmp/dir/file
RUN rm -rf /tmp/dir ; touch /tmp/dir

Here we will have both /tmp/dir/.wh.file and /tmp/dir. I guess this situation is similar to #122

The correct solution would be something like this:

1. Memorize all files we already added
2. Memorize all directories we already added
3. When adding a new file, check whether parent directory already exists or not; if it does and it is not actually a directory, skip the file; otherwise, add the file as normal