I want to parse a PHP source file, into an AST (preferably as a nested array of instructions).
I basically want to convert things like
f($a, $b + 1)
Well, you can look at the answers from Parsing and Printing PHP Code and Generating PHP code (from Parser Tokens): basically PEAR's PHP_Beautifier package at http://pear.php.net/package/PHP_Beautifier can be extended to do what you want, but it sounds like it requires some heavy lifting.
And if you're not constrained to PHP then http://www.eclipse.org/pdt/articles/ast/PHP_AST.html walks you through using the Eclipse PHP module's AST parser.