Go: basic overlay support

[nickrolfe]

This adds overlay support to the extractor, along with corresponding QL discard predicates. I have not attempted to add overlay[local] annotations to any libraries, meaning that the 'overlay frontier' is currently at the dbscheme.

Some additional notes:

• Although the extractor already supported path transformers, it needed a little tweaking to work correctly (and to not be overridden in certain cases).
• There are a few (pretty rare) cases where analysis of an overlay database will not perfectly match behaviour of full analysis, since we discard anything that is @locatable, but some entities that don't have locations (like types) don't get discarded.
• There's a bit of a hack to always re-extract cgo-processed files (and, to match that, always to discard entities in such files), since, as far as I can tell, there's no way for the extractor to know which original source file a cgo-processed file came from.

Commit-by-commit review is recommended.

[Copilot]

Pull Request Overview

This PR adds foundational support for database overlay functionality in the Go extractor, enabling incremental analysis by reusing a base database and overlaying only the changes from modified files.

Key changes:

• Introduces new database schema relations (databaseMetadata and overlayChangedFiles) to support overlay metadata
• Adds logic to skip extraction of unchanged files when building an overlay database
• Updates path handling to use transformed paths consistently across extraction and trap file generation

Reviewed Changes

Copilot reviewed 23 out of 23 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
go/ql/lib/upgrades/b3da71c3ac204b557c86e9d9c26012360bdbdccb/upgrade.properties	Defines upgrade metadata for adding overlay support relations
go/ql/lib/upgrades/b3da71c3ac204b557c86e9d9c26012360bdbdccb/old.dbscheme	Baseline schema snapshot before overlay changes
go/ql/lib/upgrades/b3da71c3ac204b557c86e9d9c26012360bdbdccb/go.dbscheme	Updated schema with overlay support relations
go/ql/lib/semmle/go/Overlay.qll	Defines entity discard predicates for overlay analysis
go/ql/lib/semmle/go/Locations.qll	Imports overlay module for location handling
go/ql/lib/qlpack.yml	Enables overlay evaluation compilation
go/ql/lib/go.dbscheme	Adds databaseMetadata and overlayChangedFiles relations
go/extractor/util/overlays.go	Implements overlay detection and changed file handling
go/extractor/util/BUILD.bazel	Adds overlays.go to build sources
go/extractor/trap/labels.go	Updates file label generation to use transformed paths
go/extractor/srcarchive/srcarchive.go	Refactors path transformer initialization
go/extractor/srcarchive/projectlayout.go	Adds environment-based project layout loader and exports fields
go/extractor/srcarchive/BUILD.bazel	Adds util dependency
go/extractor/gomodextractor.go	Skips extraction of unchanged go.mod files in overlay mode
go/extractor/extractor.go	Integrates overlay change tracking and skips unchanged file extraction
go/extractor/dbscheme/tables.go	Adds overlay relations to schema definition
go/extractor/cli/go-extractor/go-extractor.go	Adds --source-root argument parsing
go/extractor/cli/go-autobuilder/go-autobuilder.go	Passes source root to extractor and writes overlay metadata
go/extractor/cli/go-autobuilder/BUILD.bazel	Adds srcarchive dependency
go/downgrades/b1341734d6870b105e5c9d168ce7dec25d7f72d0/upgrade.properties	Defines downgrade operation for overlay relations
go/downgrades/b1341734d6870b105e5c9d168ce7dec25d7f72d0/old.dbscheme	Schema with overlay relations for downgrade reference
go/downgrades/b1341734d6870b105e5c9d168ce7dec25d7f72d0/go.dbscheme	Target schema without overlay relations
go/codeql-extractor.yml	Declares overlay support version

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[Copilot]

The pathTransformer variable being assigned here is a package-level variable, but in the context of this function, a local variable should be used instead. The function returns a *ProjectLayout, so the assignment should be to a local variable that is then returned, not to the package-level pathTransformer.

Suggested change

	pathTransformer, err = LoadProjectLayout(ptf)
	pathTransformer, err := LoadProjectLayout(ptf)

[Copilot]

The path prefix check is incorrect. It should use pkg.Dir+string(filepath.Separator) as the prefix to check, not append the separator to path. The current logic checks if path concatenated with a separator starts with pkg.Dir, which is backwards.

Suggested change

	strings.HasPrefix(path+string(filepath.Separator), pkg.Dir) {
	strings.HasPrefix(path, pkg.Dir+string(filepath.Separator)) {