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fix: npm update --save (#4223)

Previously `npm update` was not respecting the `save` option, it
would be impossible for users to use `npm update` and automatically
update their `package.json` files.

This fixes it by adding extra steps on `Arborist.reify._saveIdealTree`
to read direct dependencies of any `package.json` and update them as
needed when reifying using the `update` and `save` options.

- Uses config.isDefault to set a different value for the `save` config
  for both the update and dedupe commands
- Tweaks arborist to make sure saveIdealTree preserves the behavior of
  skipping writing to package-lock.json on save=false for install while
  still writing the lockfile for `npm update` with its new default value
  of save=false.
- Updated and added some new tests on arborist to cover for these tweaks
- Added `npm update --save` smoke test on cli

Fixes: https://github.com/npm/cli/issues/708
Fixes: https://github.com/npm/cli/issues/2704
Relates to: https://github.com/npm/feedback/discussions/270

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