reference docs: fix broken links and markdown touch-ups

- fix various broken links
- fix incorrect anchors
- updated links for content that moved, so that no
  redirect to the new location is needed.
- touched-up Markdown;
  - re-format some JSON output
  - add blank line betweeen command and command output
  - format "note" blocks

Signed-off-by: Sebastiaan van Stijn <github@gone.nl>

docs/reference/commandline/wait.md

@@ -15,8 +15,10 @@ Options:
       --help        Print usage
 ```
 
-> **Note**: `docker wait` returns `0` when run against a container which had
-> already exited before the `docker wait` command was run.
+> **Note**
+>
+> `docker wait` returns `0` when run against a container which had already
+> exited before the `docker wait` command was run.
 
 ## Examples