Use $(...) for command substitution, not backticks

Currently both \`...\` and `$(...)` are used for command substitution. It's better to chose just one and stick to it, to avoid confusion.

Some arguments favoring `$(...)`:

* **Easier to read.** The backtick is easily confused with apostrophes and quotes.
* **Easier to nest.** Nesting backticks commands is an escaping nightmare. Using parenthesis is natural: `$(foo $(bar))`