Fix Markdown warnings

[bact]

Fix warnings from markdownlint

• MD014/commands-show-output: Dollar signs used before commands without showing output
• MD030/list-marker-space: Spaces after list markers [Expected: 1; Actual: 3]
• MD032/blanks-around-lists: Lists should be surrounded by blank lines
• MD040/fenced-code-language: Fenced code blocks should have a language specified
• MD047/single-trailing-newline: Files should end with a single newline character
• MD049/emphasis-style: Emphasis style [Expected: asterisk; Actual: underscore]
  • There are 20+ instances in .md and .qmd in the repo that use *...*, compares to 2 that use _..._.

Ref: https://github.com/DavidAnson/markdownlint/blob/v0.34.0/doc/Rules.md

This PR contains:

• [X] Docs

What is the current behavior? (You can also link to an open issue here)

No change in behavior

What is the new behavior?

No change in behavior

Does this PR introduce a breaking change? (What changes might users need to make in their application due to this PR?)

No

Other information:

[jjallaire]

Thanks for this! Our markdown is sometimes hand-edited but sometimes authored with the Quarto visual markdown editor (https://quarto.org/docs/visual-editor/vscode/). This in turn uses Pandoc to write markdown, and we will just get whatever it's default behavior is (i.e. we can't actually customise it). So running a non-Pandoc based linter will probably always end up yielding errors of this kind.

So net, net I don't think we should try to fix these (btw in some cases we don't specify a language for fenced code blocks so that there is no shaded background (that is the Quarto default behavior).

[bact]

Thank you for the clarification!