Ruby: add support for extracting overlay databases

[nickrolfe]

There will need to be followup changes on the QL side before querying will work, but this is enough to be able to build an overlay database for Ruby.

[Copilot]

Pull Request Overview

This PR adds support for overlay database extraction in Ruby by introducing a new databaseMetadata relation and path‐prefix transformation logic.

• Introduces a --add-metadata-relation flag to the shared extractor generator and implements create_database_metadata().
• Adds PathTransformer and normalize_and_transform_path in the shared extractor for prefix rewrites.
• Updates the Ruby extractor to skip unchanged files, load overlay changes, apply path transformations, and emit an empty base‐metadata file.

Reviewed Changes

Copilot reviewed 22 out of 22 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
shared/tree-sitter-extractor/src/generator/mod.rs	Added add_metadata_relation flag and create_database_metadata
shared/tree-sitter-extractor/src/file_paths.rs	Implemented PathTransformer, load_path_transformer, and path normalization with transformation
shared/tree-sitter-extractor/src/extractor/*.rs	Propagated transformer through file population and trap writing
ruby/ql/lib/ruby.dbscheme	Added new databaseMetadata relation definition
config/dbscheme-fragments.json	Registered the Database metadata fragment
ruby/extractor/src/extractor.rs	Added overlay‐change filtering, transformer usage, and metadata output
ruby/extractor/src/generator.rs	Enabled metadata relation in the Ruby generator

Comments suppressed due to low confidence (1)

ruby/extractor/src/extractor.rs:347

• [nitpick] New get_overlay_changed_files logic and load_path_transformer are not covered by existing tests. Consider adding unit tests for parsing the JSON changes file and path transformation behavior.

fn get_overlay_changed_files() -> Option<HashSet<PathBuf>> {

[Copilot]

Collecting an iterator of Option<PathBuf> will not produce HashSet<PathBuf>. You should use filter_map to drop None entries and wrap the resulting HashSet in Some(...) before returning.

Suggested change

	.map(|change| {
	change
	.as_str()
	.map(|s| PathBuf::from(s).canonicalize().ok())
	.flatten()
	})
	.collect()
	.filter_map(|change| {
	change
	.as_str()
	.and_then(|s| PathBuf::from(s).canonicalize().ok())
	})
	.collect::<HashSet<PathBuf>>()
	.into()

[nickrolfe]

@aibaars do you have capacity to review this?