Output nwk filenames are inconsistent

[aofarrel]

matUtils extract -i sometimes adds a file extension to its outputs, and sometimes doesn't. Additionally, when it does add a file extension, it's not .nwk, it's .nw.

Simple example of problematic behavior

Assume samples.txt is a newline delimited text file that consists of 23 samples that are on the tree, and are reasonably close together.

matUtils extract -i tree.pb -t outfile -s samples.txt --> outfile, no extension
matUtils extract -i tree.pb -t outfile -s samples.txt -N 23 --> outfile-subtree-0.nw, outfile-subtree-1.nw, etc

matUtils extract -i tree.pb -t outfile.nwk -s samples.txt --> outfile.nwk
matUtils extract -i tree.pb -t outfile.nwk -s .samples.txt -N 23 --> outfile.nwk-subtree-0.nw, outfile-subtree-1.nw, etc

Proposed behavior

Either:
A) matUtils extract -i should always add the .nwk extension regardless of -N value
B) matUtils extract -i should never add an extension (be it .nwk or .nw) regardless of -N value

Example A

• matUtils extract -i tree.pb -t outfile -s samples.txt --> outfile.nwk
• matUtils extract -i tree.pb -t outfile -s samples.txt -N 23 --> outfile-subtree-0.nwk

Example B

• matUtils extract -i tree.pb -t outfile -s samples.txt --> outfile
• matUtils extract -i tree.pb -t outfile -s samples.txt -N 23 --> outfile-subtree-0

Affected versions

I'm using the dockerized version, yecheng/usher@sha256:sha256:2b8fa3a0c1df6844bb7dd042c9861bc6110df83b340f5b925680bdae03aee3d0 which runs v0.6.2. I don't want to be That Guy who opens an issue for an outdated version, but I can't install the latest version natively due to my setup, and it should be pretty quick to confirm if this behavior is in the latest version.