[Docs] Fix badly indented lists and blocks

[cameel]

We had a bunch of badly indented stuff in the docs that did not quite break the syntax but still got rendered weirdly.

To render a list to properly in .rst:

• There must be an empty line between a list and the text preceding it. Without it the preceding line is for some reason displayed in bold.
• There must be no indentation for top-level items (we had them sometimes indented with a single space).
• Nested items should be indented just enough to match the width of the bullet (so 2 spaces for simple - x but e.g. 4 for something like 12. x).

The PR also fixes inconsistent indents for code blocks in a few places where I've spotted them while fixing lists. Looks like Sphinx does not enforce any particular indent width here but some of our scripts (e.g. isolate_tests.py) expect 4 and won't detect code blocks with a smaller indent. There were also some blocks indented with a mix of tabs and spaces.

When reviewing it I recommend taking a look in the mode that ignores whitespace. In that mode the diff should be nearly empty except for newlines (these do not get ignored) and some changed bullet points. There's also one change that adjusts a header.