Rewrite README instructions to use pipx

[pkalita-lbl]

Fixes #81

Mainly this is updating the README to give instructions on getting set up using pipx instead of creating the "wrapper" Poetry environment.

While making sure that everything in the README works out of the box I made two additional changes:

• Updated a few of the git-related Makefile targets so that there are no uncommitted files still hanging around after the initial commit
• Removed the git-init target from install and added it to setup. There are valid reasons you might want to run make install again later and you don't want to call git init at that point.
• Removed the instruction to call make deploy from the README. I don't think we want to encourage people doing this manually especially since we have a GitHub Action that does it.
• Fixed the unit test to account for the default example file now being a collection (https://github.com/linkml/linkml-project-cookiecutter/pull/72)

[pkalita-lbl]

• Were we not doing recommit hooks in this cookiecutter?
• Do we want to include that here or some other time (different PR).

I guess we're not at the moment. It's not a bad idea, but let's make a new issue for that.