Document command line flag corner cases more clearly

[DanielTsiang]

Make README.md clearer.

Changes:

• Add more examples of how to use flags with clean and check modes.
• Rewrite flags section into bullet points, easier to digest information flag by flag instead of all in one long paragraph.
• Reorder the flags at the table at the end to put the flag before the filename, which is neater. It's also simpler to use if you're using nb-clean in the CI and you're piping notebook filenames to the command via xargs.

[DanielTsiang]

Might want to hold off merging this PR in actually until this bug is resolved:

• https://github.com/srstevenson/nb-clean/issues/255

[codecov[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Comparison is base (a7b8f57) 99.46% compared to head (4b71789) 99.46%.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #254 +/- ## ======================================= Coverage 99.46% 99.46% ======================================= Files 3 3 Lines 187 187 ======================================= Hits 186 186 Misses 1 1 ```

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[srstevenson]

Thanks, @DanielTsiang, this makes things clearer! I've added a commit to give more detailed instructions about avoiding the issue you experienced in #255. Note I reverted your change to the nb-clean 1.6.0 column in the migration table: in 1.6.0, the notebook path was passed with the --input flag and not as a positional argument, so can't be moved to the end of the command line.

[DanielTsiang]

Thanks for correcting the PR!

The README.md is a lot clearer now so hopefully a lot more people will feel comfortable using this tool in the future! 🙂