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/cp.md

@@ -90,7 +90,7 @@ you must be explicit with a relative or absolute path, for example:
     `/path/to/file:name.txt` or `./file:name.txt`
 
 It is not possible to copy certain system files such as resources under
-`/proc`, `/sys`, `/dev`, [tmpfs](run.md#mount-tmpfs-tmpfs), and mounts created by
+`/proc`, `/sys`, `/dev`, [tmpfs](run.md#mount-tmpfs---tmpfs), and mounts created by
 the user in the container. However, you can still copy such files by manually
 running `tar` in `docker exec`. Both of the following examples do the same thing
 in different ways (consider `SRC_PATH` and `DEST_PATH` are directories):