Fix Go extractor incorrectly excluding cross-module dependencies

The Go extractor was incorrectly excluding valid packages from cross-module
workspace dependencies when their relative path from a wantedRoot contained
'..' (parent directory references).

Problem:
When using trace-command or specific package patterns (e.g., ./mainmodule/...),
only the input packages' ModDirs were added to wantedRoots. Cross-module
dependencies had their ModDir excluded, causing them to be skipped during
extraction when checked against unrelated sibling package directories.

Solution:
Add ModDir to wantedRoots for all packages during type extraction, including
cross-module workspace dependencies. This ensures dependency module roots are
valid extraction targets.

Testing:
- Added integration test at go/ql/integration-tests/package-exclusion-fix/
- Two-module workspace: configmodule and mainmodule
- Without fix: 2 files extracted (config.go missing)
- With fix: 4 files extracted (config.go present)

Run test: pytest go/ql/integration-tests/package-exclusion-fix/

Author: allsmog

go/extractor/extractor.go

@@ -224,6 +224,12 @@ func ExtractWithFlags(buildFlags []string, patterns []string, extractTests bool)
 		}
 
 		log.Printf("Done extracting types for package %s.", pkg.PkgPath)
+
+		// Add ModDir to wantedRoots for all packages (including cross-module dependencies)
+		// This ensures dependencies from other modules can be extracted
+		if pkgInfo, ok := pkgInfos[pkg.PkgPath]; ok && pkgInfo.ModDir != "" {
+			wantedRoots[pkgInfo.ModDir] = true
+		}
 	})
 
 	if len(pkgsNotFound) > 0 {

go/ql/integration-tests/package-exclusion-fix/build_environment.expected

@@ -0,0 +1,5 @@
+{
+  "configuration" : {
+    "go" : { }
+  }
+}

go/ql/integration-tests/package-exclusion-fix/diagnostics.expected

@@ -0,0 +1,14 @@
+{
+  "markdownMessage": "2 `go.mod` files were found:\n\n`configmodule/go.mod`, `mainmodule/go.mod`",
+  "severity": "note",
+  "source": {
+    "extractorName": "go",
+    "id": "go/autobuilder/multiple-go-mod-found-not-nested",
+    "name": "Multiple `go.mod` files found, not all nested under one root `go.mod` file"
+  },
+  "visibility": {
+    "cliSummaryTable": false,
+    "statusPage": false,
+    "telemetry": true
+  }
+}

go/ql/integration-tests/package-exclusion-fix/test.expected

@@ -0,0 +1,6 @@
+extractedFiles
+| src/configmodule/config/config.go:0:0:0:0 | src/configmodule/config/config.go |
+| src/configmodule/go.mod:0:0:0:0 | src/configmodule/go.mod |
+| src/mainmodule/app/jobs/worker/worker.go:0:0:0:0 | src/mainmodule/app/jobs/worker/worker.go |
+| src/mainmodule/go.mod:0:0:0:0 | src/mainmodule/go.mod |
+#select

go/ql/integration-tests/package-exclusion-fix/test.py

@@ -0,0 +1,18 @@
+# Test for the package exclusion bug fix.
+#
+# This test reproduces the scenario where a dependency package in a separate module
+# was incorrectly excluded due to relative paths containing ".." when checked against
+# wantedRoots from the main module.
+#
+# Structure:
+# - configmodule/config/ (separate module with config package)
+# - mainmodule/app/jobs/worker/ (main package that depends on config)
+#
+# Bug scenario (old code):
+# When building just mainmodule packages, wantedRoots contains mainmodule directories
+# but NOT configmodule's ModDir. Checking config against mainmodule/app/jobs/worker
+# produces ../../configmodule/config (contains ".."), causing incorrect exclusion.
+#
+# Fix: Adds all dependency ModDirs to wantedRoots and prioritizes checking them first.
+def test(codeql, go):
+    codeql.database.create(source_root="src")

go/ql/integration-tests/package-exclusion-fix/test.ql

@@ -0,0 +1,8 @@
+import go
+import semmle.go.DiagnosticsReporting
+
+query predicate extractedFiles(File f) { any() }
+
+from string msg, int sev
+where reportableDiagnostics(_, msg, sev)
+select msg, sev