Overlay: Discard Java config and XML base entities in overlay extracted files

[kaspersv]

This PR improves the Java config and XML discard predicates to avoid apparent bqrs accuracy regressions under the current non-incremental Java property and XML extraction. Under non-incremental extraction, the Java property and XML extractors may extract files outside of overlayChangedFiles. To account for these files and properly discard from base, this PR extends the discard predicates to discard Java config and XML base entities in all overlay extracted files, even if they do not appear in overlayChangedFiles. The use of overlayChangedFiles is still necessary to discard from deleted Java property and XML files.

DCA experiments (variant vs baseline) shows the expected accuracy improvements for java/maven/non-https-url, java/maven/dependency-upon-bintray and java/spring-boot-exposed-actuators-config.

[Copilot]

Pull Request Overview

This PR improves overlay database handling by extending discard predicates for Java config and XML entities. The change addresses accuracy regressions under non-incremental extraction where files outside of overlayChangedFiles may still be extracted.

• Introduces new predicates to track overlay-extracted config and XML files
• Updates discard logic to handle all overlay-extracted files, not just changed files
• Creates a new abstract class DiscardableXmlLocatable for XML entity management

Reviewed Changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 1 comment.

File	Description
java/ql/lib/semmle/code/java/Overlay.qll	Adds new overlay predicates and discard logic for config and XML files
java/ql/lib/semmle/code/xml/XML.qll	Updates XML discardable classes to extend new DiscardableXmlLocatable base class

[Copilot]

The condition not files(el, _) and not xmlNs(el, _, _, _) appears to be filtering logic but lacks documentation explaining why these specific exclusions are necessary. Consider adding a comment to clarify the purpose of these filters.

Suggested change

	overlay[local]
	overlay[local]
	/**
	* Returns true if the given file is extracted in the overlay variant for an `@xmllocatable`
	* that is neither a file entity nor an XML namespace declaration.
	* The conditions `not files(el, _)` and `not xmlNs(el, _, _, _)` ensure that only relevant
	* XML locatable entities are considered, excluding files and namespace declarations which
	* are not subject to overlay extraction.
	*/