just-mr.py: Accept all tree entries for bootstrapped just

The Python script used for the first stage of bootstrapping just
uses the Git index to create trees from directories (be it file
repositories, unpacked archives, or distfiles), therefore it has
the limitations of Git itself in committing trees that contain
entries ignored by Git, such as empty directories, the .git folder,
.gitignore files and files referenced there, or other entries with
Git-specific magic names.

This commit updates the Python script to replace the use of the
Git index for importing directories to directly writing the needed
blobs and trees to the object database, then commit the resulting
top tree explicitly.

While there, fix a typing issue from our relaxed approach in using
os.environ to set the subprocess env when running commands. As on
POSIX the type is _Environ, not simple Dict[str, str], use implicit
dictionary merging (Python v3.5+) to set the Git envars. The issue
was initially flagged by pyright.

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