Improve bash completion script generation.

There are many issues with script generation. Some of them are documented in #679 & its comments.

This issue is for a first batch of bash completion script fixes.

I will submit a PR. Each commit should note the fix(es) that it contains.

After this PR is merged, I will create an issue & submit a PR for initial fish fixes, then one or more PRs for cross-shell changes, then I will resume working on more fixes.