Untrack generated files that were already gitignored

[rbardaji]

Closes #253.

The problem

.gitignore only stops untracked files from being added. A file committed
before its rule existed stays tracked and keeps reappearing as modified. Three
files were in that state:

.coverage
docs/.ipynb_checkpoints/s3_api_tutorial-checkpoint.ipynb
docs/.ipynb_checkpoints/s3_to_dataset_workflow_tutorial-checkpoint.ipynb

.coverage is the binary SQLite database written by pytest --cov. It had been
tracked since v1.0.0 and is rewritten on every local test run, so anyone running
the suite got a spurious modification in git status and could commit it by
accident with git commit -a. The two .ipynb_checkpoints files are Jupyter
editor autosaves duplicating the tutorials beside them.

None of the three are used by the API, the tests, the installer or CI.

The change

git rm --cached only — the files stay on disk. .gitignore already covers both
paths (lines 7 and 8), so nothing there needed changing and they cannot come
back.

For anyone with the repository cloned

Local copies are kept. The files simply stop being tracked after pulling; no
manual cleanup is needed and nothing is deleted from working copies.

Testing

Acceptance criteria from the issue, verified locally:

• git ls-files -i -c --exclude-standard now returns nothing.
• Running pytest tests/ install/tests/ --cov=api leaves git status clean.
  .coverage is regenerated on disk and correctly ignored.
• All three files remain present in the working copy.

Full suite still green: 1269 passed, black --check . clean across 253 files,
flake8 api/ tests/ scripts/ clean.