Let tools specify parser settings

Currently tools can only specify which parser to use (so it is selected by default) but not parser settings, which is required as well sometimes.

Start by tracing the tool configuration path where a parser is selected, then determine how parser settings could be carried alongside that selection. Done means tools can specify both a parser and its settings, with those settings applied when generating the AST; add or update coverage for the configuration behavior.

Written by the indexing model from the issue text.